Wiring Question, Snip, snip!! Options

[LowGT]

So I'm replacing my engine with another used one and it came with the original harness. As I compared it to my old one, I noticed my old one had quite a few snipped wires on it. So now I'm trying to decide if I need these wires back or not.

So, at the alternator there is the 3 prong harness and one large wire. On my old harness the large single wire has been removed leaving me with just the three prong harness. Where is this single wire supposed to go? Isn't that the wire that would carry charge back to my battery? (IMG:style_emoticons/default/blink.gif)

Two wire sets go to the starter area, one has the reverse light wires and the small gauge wire to the starter solenoid. I'm okay there. The other set has two large gauge wires in it. One goes to the starter and the other one is snipped. Where is that wire supposed to go?

My car did have the hot start "fix" installed, I removed it since I'm adding a mini-starter with this engine/trans replacement. I'm not sure if this kit install has anything to do with the snipped wires.

The further I dig, the more problems I find. It seems like the PO paid $8k to his mechanic to ruin this car.... and I have the receipts to prove it!! (IMG:style_emoticons/default/dead horse.gif)