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How is your AC wired up since the engine swap?
In a functional, stock setup, there are two things responsible for cycling the compressor. The first is the Triple Pressure Switch mounted on the AC drier. This switch will shut off the compressor when the pressure becomes too high or low. The second is the Thermo Control Amplifier mounted on the evaporator casing under the dash. The thermo amp monitors the evaporator temperature and will shut off the compressor when the temp approaches freezing.
I've been doing some research on wiring the AC for my RB s14. I was very disappointed to discover most people will simply splice some wires at the M63 plug (passenger footwell chassis interface plug). This method effectively bypasses the Thermo Control Amp and the compressor cycles off the Triple Pressure Switch alone. With the thermo amp bypassed, the compressor will keep running and freeze up the evaporator. A few people have gotten past this by slightly overpressurizing the AC Freon. The higher pressure in the lines will activate the pressure switch earlier and more often, thus allowing longer 'break periods' for the condenser, keeping it from freezing over.
I haven't yet found a schematic to properly wire in the Thermo Control Amp for an engine swap. I'll need to study the FSM and figure something out eventually.
Inspect your wiring to see if the Thermo Control Amp was wired in properly.
Test the Thermo Control Amp to verify it sends the proper signal when it approaches freezing temperatures.
If all else fails, you can use the 'bandaid' method and slightly overpressurize the AC Freon.
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