You can probably get rid of the old PCM wires. You will need to keep the hot wires and starter wires.

Can't help you with the header question.

As for the mounts, I ran the original clamshells with adapter plates I found on Ebay. Be sure to get the 1" setback plates. I ordered standard plates and installed the engine with them. It was only after the fact that I realized that I needed the 1" setback plates to get the transmission back to it's original location on the crossmember.