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.
'93 Chevy 1500 4X4 ECLB with a '99 Silverado LQ4 6.0 and '99 Escalade 4L60E. SOLD IT!!
New toy: 2001 2500 HD 4X4 Extended Cab Long Bed
John