That's a weird one. It's definitely not a fuse. When a fuse goes, it doesn't come back randomly. I would throw my vote at the motor. Is there a relay board that the motor connects to? It could also be a sticking relay. I've had an issue with an intermittent motor before. It wasn't the motor, it ended up being the relay mounted on the board that the motor connects to. Of course, I found all of this out after I already replaced the $100 motor.

Williams used EFI controller boards on most (if not all) of their motors ...

These have large copper coils on them, and they're prone to breaking.

First thing you should do is check for cracks where the coil connects to the PCB, and simply resolder it if so.

Can you try to test the defender mech in test mode, and possibly with the playfield slightly raised, to see if it works and if not, what may be holding it up? Could there be a wire shorting?

Someone else will probably have a better idea of what is causing this, but in the meantime, I would try to diagnose the problem by seeing what works in test mode. For the pops, test the coils and then if they work, test the switches. Same for the coils and switches on the shooters (are you sure the shooter coils are popping on startup and not the pass coils?). If coils are dead, check wire connections and fuses to start.