There's door lock relays and timer relays and remote relays, etc, etc, etc back there, any one of which could be causing problems. Are there any loose wires? Do you have an aftermarket alarm or remote entry. These share many of the same circuits you're having problems with.
Take a look at the electrical section of the FSM and especially the location of electrical units in that section. The foldout is a wiring schematic for the entire car. Hopefully these will help you piece her back together.
http://www.nicoclub.com/FSM/Q45/1994_Q45/
For the heck of it....Is the windows button in the shifter surround (upper left button) depressed? It will lock the windows, not sure about the doors.