99 LTD Manual Swap

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#1
Alright here goes nuthin!

Picked up a full 5 speed swap from Josh Young in Marysville, WA a few weeks ago. Dunno if he's on here or on t4r.org, but he's a handy guy to have around. Exclusively parts out 3rd gen 4Runners, and I lucked out in picking up a swap with 140k miles for a grand. Clutch is damn near new, flywheel looks solid, trans shifts crisp, j-shift tcase is minty fresh. Front and rear driveshafts, master and slave cylinders, hydraulic lines, shifter handles and knobs, clutch pedal assembly, brake pedal assembly, the works. I just realized yesterday there's also a starter in the box, so I'll probably swap that too. At nearly 300k on my rig, mine could probably use the refreshment.

I decided since I'm tearing into this shit, why not dump the 23lb factory flywheel for a 38 pounder from LC Engineering? 15 lbs doesn't seem like much but goddamn that fucker is hefty.
I considered ordering one of their upgraded clutch kits, but I have no experience wheeling with a manual, so I figured the stock clutch is a good baseline, and once that wears out, I should have a feel for what I'd desire in an aftermarket clutch. As such, a throwout bearing and pilot bearing are also due to arrive from LCE tomorrow, just so those are good to go once this pig is put back together.


As of right now, I've pulled my skids, removed some wiring that I had running through the center console, and started working on tearing apart the auto shifters. Dinner bell is ringing so I'll be back to it in an hour.
 

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#3
I always wonder if the fj 6 speed would bolt up into a 4th gen.
V8 or V6? If the 4.0L, it should. I've got a good buddy of mine, not sure of he's on here, that has an 07 6mt FJ Cruiser that's pretty damn built up, and he recently acquired his dad's 2nd gen V6 Tacoma Prerunner. He plans to swap the trans and tcase from the FJ to the Taco, 4wd and manual swapping it in one go.
 

4runner DOA

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#4
V8 or V6? If the 4.0L, it should. I've got a good buddy of mine, not sure of he's on here, that has an 07 6mt FJ Cruiser that's pretty damn built up, and he recently acquired his dad's 2nd gen V6 Tacoma Prerunner. He plans to swap the trans and tcase from the FJ to the Taco, 4wd and manual swapping it in one go.
It's the 4.0, but the electronics and shit are different from the Tacoma so I'm not sure if it's a direct swap. They never stuffed a 6 speed in the 4th gen.
 
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#5
Ended up just going to bed after dinner last night, so no further progress was made. Thus far today, I moved the evap mess out of the way, pulled a bunch of wiring out of the way that I'd ran through the space where the clutch and master cylinder will go, and began rerouting those. I have a template from snotaco that I used to mark where I'll be drilling to mount the master cylinder.

Also got the center console and shifters pulled out, that was much more of a pain in the ass than I expected.

Sway bar has also been removed, by means of broken bolts that then had to be extricated by an angle grinder. Cue up endless amounts of shit finding their way behind safety glasses to my eyes, but I'll be getting new mounting brackets from Josh Young later on.
 

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#7
Got the transfer case out, and started working on getting the trans out. Can't get a couple of the bellhousing bolts out, hopefully get those pulled and the transmission out tomorrow, along with installing the clutch pedal and master cylinder.

I'm an idiot and had my new throwout and pilot bearings sent to my apartment address I use while I'm at school 6 hours away. Realizing now what a bitch of a job this is, I'm probably going to organize a return/exchange with LC Engineering for one of their street clutch kits and have my roommate return the bearings on my behalf.
 

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#9
Support trans on a jack and remove trans crossmember. Slowly lower jack a little bit to get better access to the top bolts. Use as long of an extension as you can.

I've never pulled a trans on a v6 toyota, so I can't be positive that's the easy way.
 
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#10
Support trans on a jack and remove trans crossmember. Slowly lower jack a little bit to get better access to the top bolts. Use as long of an extension as you can.

I've never pulled a trans on a v6 toyota, so I can't be positive that's the easy way.
That's how we were going about it yesterday, think I need to find a few more extensions since I couldn't break any of the top bolts loose.
 
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#11
Ended up just going to bed after dinner last night, so no further progress was made. Thus far today, I moved the evap mess out of the way, pulled a bunch of wiring out of the way that I'd ran through the space where the clutch and master cylinder will go, and began rerouting those. I have a template from snotaco that I used to mark where I'll be drilling to mount the master cylinder.

Also got the center console and shifters pulled out, that was much more of a pain in the ass than I expected.

Sway bar has also been removed, by means of broken bolts that then had to be extricated by an angle grinder. Cue up endless amounts of shit finding their way behind safety glasses to my eyes, but I'll be getting new mounting brackets from Josh Young later on.
Im literally doing this swap right now as well! where did you get the template for the master? Online or did you get it from someone in person? Im about to start doing all the little odds and ends today and maybe put the manual trans and tcase in. I have both driveshafts as well off of a manual, however the PO of the parts didnt use a match mark on the drive shafts and the front one is disconnected.... fuck. Im wondering if i should try to run it, or just take it to a driveline shop and get it balanced.. ill follow your thread and update my build thread as I progress through the swap, did you get a manual harness? Ive got the harness and ecu but all my parts are off of a same year truck ( 2000 ) and i've been told all my connectors are the same ill just need to wire in the clutch pedal, whats your course of action with wiring?
 
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#13
She runs and drives!

Between the 38lb flywheel and 4.88s with only 295/70/17s, she's hard to stall.

Just about everything bolted up no problem, the only cutting to do was there in the center console. Picture attached.

Currently I have the transfer case that came with the manual in, but later today I'm going to swap that back out with my original multimode tcase - that's how I wanted to do it all along and then for some reason decided to say, "fuck it" at the last moment, and after thinking it over last night, I'd rather have the multimode and be happy that I did that in the long run. Currently with the standard j-shift case, the computer has no clue what's going on with the t-case, as there's only 2 plugs on it, for 4hi and 4lo, as opposed to the 6 on the multi-mode tcase.

Now let's talk about wiring, and I'll attach diagrams as well. I could not, for the fucking life of me, get my rig started by just connecting the two wires off of the neutral safety switch that would indicate neutral. It showed neutral on the dash, would not fucking start. Tried different combinations, got every other gear to show up but it still would not start in neutral or park. I was starting to wonder if I'd overlooked something somewhere else, left something unplugged, fucked something up... That'd be my luck.
I'd cut the plug off the harness for the neutral safety switch, and after talking to a buddy of mine, he suggested pulling the neutral safety switch off my old auto and wiring it back up, setting it so it showed neutral.

Went to start it... And it tried to start! But after sitting for weeks only being unlocked and locked with the alarm and shit... The battery was dead. Brought my little old TDI Jetta up to jump start it and finally brought her to life. Threw CELs for shift solenoids A and B, the transmission temp sensor, and there was one other that I don't remember but it hasn't come back since I cleared the codes.

Back to wiring - I don't really want to leave the neutral safety switch attached, and that same buddy of mine has his wired up so that the ecu simultaneously thinks it's in neutral and drive, also bypassing the clutch depress and release switches, such that it can be started, and also use cruise control. Figuring out which wires are which has proved to be a royal fucking pain in the ass, as Toyota has changed the wire colors nearly every year of the 3rd gen 4runner, and God forbid they use the same wire colors between same year 4runners and tacomas, right? Couldn't find anything specific to my rig after hours spent searching online. I did find an electrical wiring diagram for the neutral safety switch for a '96(I think?) Which shows the pin numbers on the plug, along with labeling them on the wiring diagram. Both will be attached. However, there's 10 pins on the plug, 9 of which on mine are used. The diagram only has 5 of them labeled, the rest are blank. Lucky for me, that same buddy of mine works for a Toyota dealership and able to dig up an EWD for the 1999 model year 4Runner, with correct wire colors (attached). HOWEVER, it still doesn't show the black w/ white stripe and solid black wires that are in pins 5 and 6 as I have labeled in the second photo. Oh well.
 

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#14
Continued:

I disconnected the black w/ red and black w/ white wires from the NSS plug and wired them back together, which indicates neutral on the dash, with the NSS unplugged. No crank, no start, nothing. Plugged in the NSS.. fired right up. Disconnected the black and black w/ white wires from the NSS plug, wired them together and unplugged the NSS - fires right up. My buddy said he wasn't able to find anything regarding what those wires are, but being that my rig is a limited, I'm figuring that those two wires are probably connected to the immobilizer possibly? Regardless, I've got it started now, and that might be an idea for a killswitch.

That's where I'm sitting at currently.
 

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#16
This is awesome! I have a multimode im waiting to throw in because I need to pull an actuator for it from the junkyard. Have you took it offroad yet? I took mine to the sand dunes the day after I finished the swap and it was extremely satisfying, but the trans itself moves a lot more than the auto did when taking on violent terrain. I got lucky with my swap and did a 2000 to 2000 both trucks SR5's mine was basically 100% plug and play but as of right now i still just have the two wires connected on the old neutral safety switch. 4WD low with the manual is EXTREMELY low gearing compared to the auto as well. I bottomed my truck out in some mud and with this manual trans I put it in 4x4 low and my X-Comp's dug me right out. I was impressed. Congrats on your success!
 
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#17
This is awesome! I have a multimode im waiting to throw in because I need to pull an actuator for it from the junkyard. Have you took it offroad yet? I took mine to the sand dunes the day after I finished the swap and it was extremely satisfying, but the trans itself moves a lot more than the auto did when taking on violent terrain. I got lucky with my swap and did a 2000 to 2000 both trucks SR5's mine was basically 100% plug and play but as of right now i still just have the two wires connected on the old neutral safety switch. 4WD low with the manual is EXTREMELY low gearing compared to the auto as well. I bottomed my truck out in some mud and with this manual trans I put it in 4x4 low and my X-Comp's dug me right out. I was impressed. Congrats on your success!
I haven't driven it other than around the block yet, but that has proven very satisfying in itself. There's a list of things I need to wrap up, including finding a plug to connect to the reverse switch because for the life of me, I can't figure out a part number for it. Also, what did you do for the check engine codes for the shift solenoids? I figured I'd put a volt meter on the shift solenoids in my auto and buy corresponding resistors.

I still need to put my sway bar back in, worn out suspension that was never meant for a winch and bumper makes the front end very soft, and not in the good way. Need to get my driveshaft lengths corrected too.
 
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#18
I haven't driven it other than around the block yet, but that has proven very satisfying in itself. There's a list of things I need to wrap up, including finding a plug to connect to the reverse switch because for the life of me, I can't figure out a part number for it. Also, what did you do for the check engine codes for the shift solenoids? I figured I'd put a volt meter on the shift solenoids in my auto and buy corresponding resistors.

I still need to put my sway bar back in, worn out suspension that was never meant for a winch and bumper makes the front end very soft, and not in the good way. Need to get my driveshaft lengths corrected too.
For the reverse switch are you talking about a wiring harness plug, or a new reverse switch in and of itself? I know the reverse switch can be found on rock auto. If youre looking for the connector to add into the wiring harness maybe just google two prong toyota connector. Something like this may help https://www.amazon.com/Connector-2-way-Toyota-Signal-90980-11162/dp/B01E3C6YS2 . You swapped over your ECU and still have check engine light for the solenoids? I've got a CEL but im not sure what its for, i havent read the code yet. Buying resistors is a great way to overcome that. Your front driveshaft from what I understand can be used, the rear can also be extended, i've got both manual shafts, however i've seen a guy use an aluminum spacer for the rear driveshaft between the pinion flange on the rear diff and the driveshaft itself and he said he had no issues with it. For what its worth the manual driveshaft for the rear is a lot beefier than the auto driveshaft. I've been busy with school and work, I have yet to complete the wiring on my truck. I've got a manual ECU in, if i still have a CEL for a shift solenoid on the auto harness with a manual ECU then that will be straight up weird, the solution i can think of is finding out which pin those solenoid wires lead back to and unplug the fuckers, manual ECU shouldnt be checking for a solenoid anyways. Im not sure if its that simple but fingers crossed. I havent even fixed my parking brake yet, ive got about 1200 miles on the swap.
 
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#19
btw I was just thinking about this, I dont think youll need to swap your rear driveshaft out if you put the multimode tcase in because the multimode is substantially longer than the jshift and might make up for that extra distance.
 
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#20
For the reverse switch are you talking about a wiring harness plug, or a new reverse switch in and of itself? I know the reverse switch can be found on rock auto. If youre looking for the connector to add into the wiring harness maybe just google two prong toyota connector. Something like this may help https://www.amazon.com/Connector-2-way-Toyota-Signal-90980-11162/dp/B01E3C6YS2 . You swapped over your ECU and still have check engine light for the solenoids? I've got a CEL but im not sure what its for, i havent read the code yet. Buying resistors is a great way to overcome that. Your front driveshaft from what I understand can be used, the rear can also be extended, i've got both manual shafts, however i've seen a guy use an aluminum spacer for the rear driveshaft between the pinion flange on the rear diff and the driveshaft itself and he said he had no issues with it. For what its worth the manual driveshaft for the rear is a lot beefier than the auto driveshaft. I've been busy with school and work, I have yet to complete the wiring on my truck. I've got a manual ECU in, if i still have a CEL for a shift solenoid on the auto harness with a manual ECU then that will be straight up weird, the solution i can think of is finding out which pin those solenoid wires lead back to and unplug the fuckers, manual ECU shouldnt be checking for a solenoid anyways. Im not sure if its that simple but fingers crossed. I havent even fixed my parking brake yet, ive got about 1200 miles on the swap.

I was talking about the plug itself, that comes off the wiring harness. I ended up scoring one from a junkyard in Buckley, WA, and it worked out perfect. Just extended the wires from where the neutral safety switch was and we're golden.

As for wiring harnesses and ECUs, I did NOT swap anything over. I jumped the wires as needed to get the truck to think it's in neutral all the time, think it's in drive with the clutch out (read neutral and drive, but the computer is cool with that) and think it's in reverse when I throw it in reverse (read neutral, drive, and reverse with the clutch out).

My check engine light is for the shift solenoids, and an incorrect resistance since the resistors I bought are 20 ohm, and the EWD I got my hands on via my Toyota parts contact shows it should be 13 ohms. Even so, there's 3 wires that come out of the shift solenoids plug, all positive leads that would need a resistor wired in and then to a ground. There's no ground in that plug and I've got no fucking clue what to ground it to, so if you've got ideas, I'm all ears. For now I'm just living with the CEL, it drives just fine.

You are correct, I reused my front driveshaft with no issues, other than I installed the front end first like an idiot and then had to fully compress the slip yoke, pushing out all of the grease onto myself, to get it over the studs on the transfer case flange. But it works. My rear driveshaft was already custom built by Tom Woods, so I sent it back to them to have them lengthen it, partially for peace of mind since I'll be doing new suspension soon ish and I expect to net another inch to inch and a half of lift on top of what I have already.

My only complaint now is that since the manual is geared lower than the auto, even in 5th gear, I'm running 2600rpms on the highway at 62mph. Time for 35s
 
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