I just read through and it sounds like you had the "typical" problems with a R-n-R. I was wondering a couple things though. 1, did you get a roller HO cam in there (or did you find the HO firing order was the correct order for your engine?) and 2, did you replace the battery and get it fired yet? If you replaced the cam, I hope you also replaced the lifters and even rockers at the same time. Makes a good difference impo.
Oh, and that pic in post 7 resembles an air injection(smog) pump crossover part. That allows for added air and thus, added o2 to enter your system allowing for better emission readings. When stock, there was almost certainly a pipe running from the rear of each cylinder head with that pictured piece on each head, connecting the pipe. It has also been called the thermactor pipe. Instead, yours may be solid and used as a block-off. You can probably still purchase the (5/8" I think) plugs from Ford if you don't wanna re-use that bolt, etc. They screw in flush and things look normal.