Yes the 3rd ecu plug cut it out of the body loom , but to save yourself some time cut it after the fuel open circuit relay which is on the ecu. I follow the ae82 wiring when getting constant power to the ecu and tap into the brake switch.

As for the fuse box in the bay, if you trace the wires you will find them to be alternator wiring and thermo fan that goes in there. If you rip the loom apart and remove all alternator wiring it is the neatest way of doing it.