Here are the instructions from the manual, this is for a '93 Explorer:
Programming Transmitter(s)
To program (or re-program) transmitter(s) into the remote entry module, perform the following steps:
1. Turn ignition switch to ON or ON/ACCESSORY position and momentarily short the two terminals of the Program Connector (J4) (a two-pin connector taped to the wire assembly and accessed by removing the LH quarter access panel). All doors should lock then unlock. Remove shorting pin.
2. Press any button on transmitter. All doors should lock then unlock to verify the transmitter has been programmed.
NOTE:
If door locks do not respond, press button again (up to three times maximum with the same transmitter). If door locks still fail to respond, go to «Pinpoint Test F.»
3. Repeat Step 2 to program additional transmitters into the control module (up to four transmitters maximum).
4. Turn ignition OFF. All doors should lock then unlock.
5. Check operation.
NOTE:
The remote entry module erases all previous transmitters from memory when the transmitters are programmed or re-programmed. The remote entry module can store up to four transmitters in memory.
Also including this for the Program Module
Remote Entry Module Connectors
There are four connectors to the module: J1 (26-pin), J2 (16-pin), J3 (antenna), and J4 (program connector). Connectors J1, J2, and J4 have the pins laid out as shown here.
Hope this helps!