Swapping a 99LS1 and t56 into my 89 iroc that was originally a 305 tpi 5 speed, I have a painless harness to run the engine and I know where all those connections go, my question is what do I do with all the wires on the driver side of the car that run the wipers and other accessories?

 

The other side of the c100 (non engine stuff) stays intact.

 

So that side of the harness doesn't need to be cut or anything, I just have to cut the side that runs the engine and join the painless harness into that?

 

Yep

Here is the 89


You will still need to run fuel, possibly back up lights etc..

https://www.thirdgen.org/forums/ltx-...formation.html

 

You didn't ask the question you meant to ask. Try again with more clarity.

 

Read the 3rd gen harness prep thread

The painless harness will be a stand alone, so you need to extract the power/gauge/HVAC wires from the C100 and discard the old ECM stuff