also there are two bolts on the top of the bellhousing that are a pain in the BUT to get in/out, i still need to put those in
WHAT!!! you drove without 1/5 of the bolts properly on?!?!?!?!
ill give you a hint, put a jack under your cross member, unbolt it from the frame and drop it an inch or two, then get two long socket extensions and 2 or 3 small ones. put those bolts in from where your shifters poke threw the body.
Ok, to your problem. its an efi engine correct.
where is the motor from, company?
I would start by looking at any hose or wire near the header, you had to disconnect a couple things from the area to stick a header in there.