Correct me if I'm wrong:
Door switches: Always functional.
Fob locks: Two fobs always set alarm, always unlock, always pop trunk, lock doors intermittently.
It doesn't hurt to pop apart the fobs and make sure the battery clip is soldered in nicely and clean all the contacts. Otherwise, yeah, it sounds like you've got some footwork to do on wiring. Might get lucky with an obvious wire rubbed open.
Unless you've got a spare Remote Control Door Lock Receiver/Compass sitting around to swap in.