Car idles as if misfire and cat converter overheats

Hello, I'm a mechanic and have been stuck on this one car for nearly 2 weeks now. Initially the car came in for a blown motor. We replaced the motor and everything was working smoothly, only the transmission wouldn't shift. So we replaced the trans after determining no other possibilities. Upon reinsertion of the motor and trans the vehicle now runs roughly, as if shorting out. All fuses are now good, though I did have fuse #9 in the fuse box burn out multiple times. After tracing the several wires, I found 2 damaged relays (overheated and melted).

But for the time being all fuses and relays are within proper operation. I tested all fuel injectors, replaced spark plug, checked for blocked muffler and cat, checked for bad mounts. But none of these are the problem.

I'm wondering if the wiring from an injector or perhaps the circuit path of fuse #9 might be causing this issue? Any and all insight is welcome.

(please ignore the yellow highlight, this was the only valid image I could find. It is fuse #9 that had the problem)