here's basically how I did mine on my 94 model 2wd that had a V6 in it originally


the wiring you need to worry about keeping is the AC, oil pressure and coolant temp wire, label all these as you unhook the stock harness from the engine. I left the entire stock harness in place until I had my swap completed. I then installed my LSX engine and transmission.. I used a harness from nelson performance as well... I mounted my computer under the hood and put my new harness on the engine and trans... I hooked up my ac wiring to my original compressor, hooked up my oil pressure and temp gauge wires. I ran the wire for the diagnostic port inside and mounted it where the original port was mounted. I ran the wire for the check engine light, speedometer, tach from the nelson harness into the cab thru the fire wall and connected them to the correct place in the original dash harness plug for my cluster... other than that you hook up the power and fuel pump wires for the aftermarket harness and you will be good to go... I do not have a show truck and was not worried about leaving the factory harness in the engine bay... As far as the rest of the original harness plugs that were not used I cut off the ends, put heatshrink on the ends of the wires and tucked them into the wiring loom to clean things up...