The a/c system in the Baja isnt anything unique. Its just like any other Subaru a/c system. You will have better luck posting in the Service/Maintenance forum since this is not really a Baja-unique problem.
But, if I had to take a guess I would say that the fan relay or a/c clutch relay is bad. Probably shuts off when it gets hot and turns back on when it cools off. JUST a guess though.