I'm not really sure. The deck was replaced with a Sony M730 Xplod, which included the wiring harness. In the front I have Alpine Type-R componants. What it looked like when I had the door panel off was that all the wiring from the crossover to the speakers was new (included with the Type-Rs). I believe the wiring from the crossovers to wherever the wiring comes across into the door is new. There's some kind of a molex connector (?) there which I assume is still there from stock. The in back I have Type-R componants. The wiring used for that I don't know. I assume it's stock.
My window and power locks work fine, so I don't think it has anything to do with the car's electrical system, unless I need something like grounding.
The wiring for the deck looks pretty ghetto now that I think about it. Between the car and where it mates with the deck it looks like all the wires have been spliced, so one type of connector wires up into a different type of connector at the other end. It has some electrical tape wrapped around the whole deal. Is it supposed to be like that?