Found the problem and believe it or not it was one of the easiest fixes ever.
I started looking at the wiring diagrams for the eccs and really couldn't find much to check except for some fusible links and what not. I stumbled across something in the fsm saying to keep the ecu at least 10cm from any other part of the harness to avoid noise from other wiring. I moved the ecu back to where it belongs and pulled all the harnesses away from it and sure enough it worked exactly like it was supposed to. I'm guessing that this has probably been the problem with the car not starting since the start. Even when I tore it down and retimed it...as crappy as that is.
So, in short, keep your ecu where it is and don't have any wires around it.