Man you have a real mess on your hands. I just started reading your post, that set up don’t seem to be done by any racers. Throttle body is the stock 55mm, and I don’t see the ECT sensor anywhere. And seem to have an aftermarket fuel rail, does it has a t least a fuel pressure regulator?
I think you need to start from scratch, I’m sure a few critical electrical connectors are gone.
Good luck with your project, but I would suggest you to start from zero