the way to protect the wires, would be to do two things, especially if youre making your own wires, get the long strait boots rather than the 90* boots, they are a bit harder to get off when you want to, but they should get past your header pipes just fine. but also there are fiberglass sleeves you can buy, that are only like 6 inches long, that slide down the wires and give you insulation between the wires and pipes.
also, is this the engine with the 4 hole spacer?? id take that off personally.