I'll do my best to answer your questions RRanger.
You have a few options for wiring... The gas and diesel have very different wiring harnesses. The gas has a wiring harness for all the lights and bells and whistles, and then a wiring harness that runs from the ECM and tells the carb what to do and does all the emission stuff. The diesel truck has everything combined into one harness.
Your options...
1. Completely remove both wiring harnesses from the gas pickup and put the diesel one in its place. It will only be a pain, in my opinion, when you start going towards the rear of the truck towards the taillights. Not a bad option though.
2. Remove the ECM wiring harness from the gas truck, leave the main harness, and then rewire the necessities for the diesel to run properly.
I went with number 2 and here's why. A lot of what is coming from the computer in the diesel truck has to do with the fuel sensors. Attached to the fuel filter is a probe in the top and one in the bottom and there's another one somewhere in the fuel system. Those never worked in the past so I just didn't worry about them. My diesel harness had also been molested by previous owners and so there were a few rats nests along the way, plus a poor job of wiring for trailer lights. I wanted to keep it clean.
I swapped over my dash cluster thing so that I could keep track of the mileage but also have a tachometer since the gas truck didn't have one. So I had to wire the tach, fuel cut off switch, glow plug switch, and I did a few others that I wasn't totally sure what they did. Some day in the near future I'll try cutting those questionable wires while the truck is running and then turn it off and back on again to see if they are even necessary. The unknown wires were accounted for in the wiring diagram but I didn't know if they were necessary for the truck to start and I didn't want to take a chance. I just wanted the truck to start. I'm planning to eliminate as much as I can to keep it very simple.
I had to cut a whole in the firewall to get my fuel filter to bolt up to it. That was really only a pain because the place I wanted to mount it was also the same place that the cable came through for the previous mechanical clutch cable. I removed that with a air chisel and then welded a new piece for my fuel filter to bolt to. It wasn't too bad, and I only started a small fire in the process.
Lastly was the clutch pedal since the diesel transmission has a hydraulic clutch, and the gas has a mechanical clutch. It really wasn't too bad until I went to mount the actual clutch pedal. The little master cylinder wasn't too bad. I cut a big hole with a hole saw and made some measurements and got it mounted. The clutch pedal though has a bracket to support it so there isn't excessive pressure on the firewall... that was a pain in the neck.
If you decide on option 1 for the wiring harness, make sure to install that clutch pedal bracket while there is no wiring in the way. I got it done but it was probably my least favorite part of the whole project and I may go back to it again someday to make some modifications. Wish I had had a plasma cutter.
My truck didn't have an intercooler. I know that some of the 4D56T's came with them but mine doesn't and I had thought about putting one on at the beginning of my build but I already have a lot connected to the radiator support with the oil cooler, air conditioner, and radiator. I'm afraid I'd be loosing good flow with one more thing in the path. I'm fine with how it is for now.
Otherwise, I used the drive line and rear end from the gas truck.
I went to put the skid plate that came on the gas pickup and discovered the oil pan on the diesel is a tad bigger so I'll have to cut it some to get it to mount properly. Otherwise it really isn't very complicated. For the 2WD, the transmission cross member was the same so that made it easy. The mounts were the same too and the one from my diesel was really beat up so that was a win!
I did have some wiring for the starter, as the battery from my diesel was behind the cab. I just talked about that though a few posts ago on the thread.
I could probably ramble on, but I'll end it there. Let me know if you have anymore specific questions.
I'm lucky I have the diesel truck to sit beside the gas one as I change it over. Piece by piece. Its looking like from your post, the order would be
1)remove gas drive train
2)Install clutch pedal and hydraulics.
3)Wiring
4) drop in Motor and tranny.
5)hookup.
Going to run it on gas for a bit and then decide if its a plan to go diesel.
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