The first thing that you should do is remove your home-made fusible link, read up on fusible links, and make or get a new one. Once your wiring burns up, you're in a whole new painful world, if the car survives. (Nevermind, you edited out your 10 gauge wire remark. Did you just switch from 10 gauge to 60 amp wire? You shouldn't use a higher capacity wire either, get some 40 amp).
Edit - if it's the green one from the battery, it's the EFI harness power.
Proper fuel pressure is key to the EFI system. Measuring that would be good. Intermittent problems are hard to diagnose though, so your occasional "bog" could be difficult to cure.
And the pump running could be due to someone bypassing the contact switch in the AFM or actually bending it so that it stays closed all the time. You can pop the black cover off of the side of the AFM to see how it's working. Someone might have rewired the pump power also.
Reading the Engine Fuel section in the service manual will save you a lot of time and money, in the long run.