Sorry I can't help you much, but just to let you know that my '88 also runs when you take the main fuel pump fuse out. I wanted to relieve the fuel pressure for a repair I was doing and tried to shut the main pump down, and couldn't do it by removing the #7 fuse! I ended up disconnecting it at the pump to shut it down, though if I knew what I was doing back then I'd just take the #5 fuse out to relieve the fuel pressure.

Perhaps wanting to remain in denial, I didn't investigate the fuse situation, so I don't have an explanation for you, or even a theory. But in my case I'm not too worried about the wiring harness. I'm just posting this to tell you to relax; if your car and mine have the same thing going on, and mine functions perfectly well, then there's probably an explanation for it. Maybe this weekend if it's warm enough I'll get under there and figure it out.

Do you know your fuel filter and fuel pressure regulator are both good?