Sounds to me like you might be in a little over your head with the "wires". Unless you have a good working knowledge of automotive electrical and computerized engine management systems, you're probably going to have a very hard time figuring out how to make the factory harness work. I have done several LT1 swaps, using various year model engines from all three platforms (
B-body, F-body and Y-body). Weeding the factory harnesses out and simplifying them for these types of swaps is not an easy task and its really not something a shadetree electrician is going to have much success with.
I suspect you are going to have a couple of options. 1. You could send your harness to someone who is experienced with this sort of thing and pay them to weed it out for you, or 2. you could just purchase a custom harness from someplace like Painless Wiring, etc. I'd offer to do it for you, however I'm kinda tied up in Mongolia right now...lol. Would prolly take DHL 8 weeks just to ship it to me over here where I am.
Lastly, here's a few tips for you for when you do get ready to embark on this swap. Buy a brand new opti-spark and install it on the engine before you even put it in the car. Also buy a new IAC valve. You are going to have problems with both of those items right off the bat, especially if your LT1 has been sitting up for any length of time. Other items you may also have problems with are the coolant temp sensors and probably the water pump (leaking at the shaft). I would also recommend pulling the intake and installing new intake gaskets.
Edit: If you'll post up the service number on your PCM, I'll look around and see if I still have some good links to the pinout diagrams and schematics for it. You may find that helpful.
Oh, and one more note I just thought of - unless you're willing to spend a chunk of change on some custom equipment, you're not going to be able to make your speedometer work unless you go with a different transmission than the 4L60.
You wil also have to have the VATS system in your PCM disabled before you will be able to run the engine...unless you still have the donor car WITH the keys. Then you can measure the resistance value in the key chip and just wire in a resistor. Otherwise the VATS will have to be disabled via custom tune.
