Just fix the stuff you found and go from there. Sounds like you need to disassemble the molded electrical connectors and clean the connections. After-all, it's 26 years old, plenty of time for corrosion to do its work. And just because you clean it doesn't mean the wire has not parted-company someplace inside the pvc jacket! Use a buzzer continuity tester on your multimeter and flex the individual wires outside of the plastic connector block (remove the wires from the connector block w/a thin blade screwdriver) to check for unseen internal breaks, the insulation appears intact, but the conductor breaks. You may be surprised at what you cannot see but that which is broken inside, causing your sporadic operation. I had that exact problem on my FZR1000, which is roughly-comparable in age. One of the fuel pump leads was broken internally at the point where the crimp was (stock fitting) and caused the pump to run intermittently.
I use a variety of wire brushes on my Dremel to clean both conductors. I also am going to try some baking soda in my Harbor Freight media blaster on some connectors.
I use a variety of wire brushes on my Dremel to clean both conductors. I also am going to try some baking soda in my Harbor Freight media blaster on some connectors.