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If the doors lock from the interior drivers switch you need to look for a break in one of the wires between the "remote antitheft personality module/RAP & the door lock relay. The RAP module is used only when you lock the doors with the remote.
For this you need a good set of door lock wiring diagrams.
The best wiring diagrams are the Ford factory wiring diagrams. About 40 bucks from helminc.com.
I have the factory diagrams for my 97, but dont know if yours is wired the same or not.