multiple electrical issues, windows, locks, interior lights, trunk release

A Ford IDS diagnostic tool would be pretty much necessary to perform the testing needed to figure out what's going on here. Has the REM been installed using PMI (Programmable Module Installation) procedures? Beyond that - since you had heavy water intrusion in the trunk, I would suspect water damage to the battery junction box (BJB) which is located in the trunk by the spare tire and battery. You may have damage and corrosion and at the very least -- could be quite wet and needs dried out. The BJB is where you will find circuit protection to the windows and locks.

discovered no ground to relays i BJB. splice s407 corroded in half. located inside wire loom between BJB and r inner 1/4 panel. have to cut the harness open to locate it. one each ground comes out of FEM & REM to supply ground to 4 SSB relays.