Cut holes in body/door for power windows and door locks. I used hole saws for this. While punches would give a cleaner cut, I didn't want to spend $100 + for punches. If you use hole saws you should use new ones. Also sand the edges of the holes to remove sharp edges that could cut the power window feed through.
I started hooking up the engine wiring harness before installing the headers. There are connections down low on the engine that are hard to get to once the headers are installed. It's also easier to hook up the starter before installing headers. There is clearance to remove/install the starter with the header installed, but I took the easy way and wired it before installing the header. The driver side was no problem, but ran into a problem on the passenger side.
I had clearance before, but raised the engine slightly on the driver side for tie-rod clearance. Now the passenger header rests against the frame. I'm stopping for now while I decide what to do. Putting a dent in the header pipe is the most probable solution.