There's your problem. In order for the "just unlug the compressor and put your AC on in the Jeep" trick to work your AC system must be properly charged with freon. '97 and later (maybe even everything after '91 I didn't look) has a low and high pressure switch in the AC lines so that the compressor will not run if the system is either over or under charged. If it does not sense that the system charge is correct it will not cycle the compressor and therefore not turn on the cooling fan.
If you would like this to work you have four choices.
1) Fix your AC system. I know that's very unlikely
2) Put a switch on the dash and activate a relay that bypasses (actually jusps the contacts)the fan relay in the fuse box. Switch on, fan runs all the time. Switch off, fan system works with the ECU as normal.
3) Run a wire to the PCM to fake the system into thinking the AC system is charged normally. From my diagrams it looks like it should be the Blue with white wire going into the PCU (wire 22 of connector 3). It should be grounded. Then the fan will run any time you turn on the AC. Disconnect the AC clutch wiring as suggested because you don't want the compressor running with no freon in the system.
4) Find the AC pressure switches in the system and install a jumer in their place. Will work as described in 3.
HTH,
B