So I assume it runs perfect when cold.
When started cold(without touching gas pedal) the RPMs go up to 1,500+ and then come down to about 1,100rpms, thats the IAC valve, ECT sensor and Computer all working correctly.
Idle RPMs should steadily drop to about 750(automatic), 650(manual) after engine is at operating temp.
After warm up is the only time you have a problem.
1994 3.0l still used the TFI ignition system, so a distributor and single coil setup.
These commonly had warmed up ignition problem, usually the TFI module on the distributor.
Good read here on checking TFI system: Ford EEC-IV/TFI-IV Electronic Engine Control Troubleshooting
One trick to test module, after warm up and a problem is occurring, shut off engine and put a bag of ice on the TFI module for a few minutes, then remove bag and start engine, if it seems to be running better replace module.
Coils can also become heat sensitive, but they take longer to cool down, they are not too expensive so replacing the coil on this type of system every 10-15 years is not unusual