So, I'm a shade tree mechanic, literally. I have two trees I work under. My buddy puttered in the yard in a 99 Tacoma few months ago and asked me to fix his truck. Too lean code, random misfire, so I dig in. O2 sensors not responding, weak ground at the coils, there's oil spitting out the half moon dual cam plugs under the valve over. The evap has been smoked, no leaks. I'm guessing that air is coming in through the pcv valve after the MAF sensor, smoke machine didn't catch it, there's your too lean code. Mind you, this has been to 4 mechanics and guy has spent 4k over the past 2 months, replaced every part they could think of, "needed it anyway" and he's here looking for some help. Pulled the valve cover, rtv on the rubber plugs, O2 sensors pulled, tested lines and no 5v reference, no pulse, heater lines good. Coil wires trace back to a melted mess by the coolant temp sensor, cut it all out, replace it. Test the circuits and still has a short somewhere, I keep going, and there are parts stacked up like dead bodies, starter, alternator, shift lock computer, stereo, ac switch, blower motor, cam position sensor, ecu, horn, signal flasher, starter relay. There's no rhyme or reason to it, just pops up wherever and fries stuff. I've got everything unplugged, dash out, HVAC out and it's still showing a short on the ecu circuit which is two wires, black and yellow stripe coming out of a 15 amp fuse. I unplug all the grounds in the engine bay and I'm about to give up. I touch the motor with no grounds attached and get a faint light. I look down and I had missed the ac compressor clutch, one more fried dish. I pull the harness, it's an old rag with browned out copper and cracked insulation with some compromised connectors. The coolant temperature sensor is broken in half. He drove this to my house. He can't afford a harness after buying all these parts, which are sitting in boxes, so I volunteer the generous idea of me build him a harness from scratch. I'm building it on the truck and things are not matching up at all. Lo and behold, this 99 pre-runner has a Tacoma ecu for a 99 and the motor is a 97 4 runner. Both 3rz -fe, but I'm guessing different pins? I've built the harness from pretty much tracing cowl wires and the abbreviations off the old ecu and pieced together wiring charts. I'm taking the advice from haltech YouTube vids for grounding. What else am I in for? Anyone done this before?

 

Sounds like overall you have an excellent grasp of things.
What you really need is the appropriate factory wiring diagrams that would show any differences in wire colors and pin=outs
There certainly are differences both between years and models.of trucks that you are dealing with stuff from.

Good luck!!