Possible that you have lost refrigerant and the low pressure switch is shutting down the compressor to protect it.
Check the accumulator (receiver/dryer) located lower, left of the radiator. Prior to '99 Ford wrapped it in an insulaing blanket that trapped moisture and caused it to deteriorate. Cut the insulation off and see if it is rusted through. Cost me about $75 US for the part and a couple of cans of refrigerant. If you don't have access to a vacuum pump to evacuate the system, you want to have it done by a pro.
Replaced mine a couple of years ago and it has been fine since.

AL


Red '98 SVT E0 3098/6535 DMD other stuff and a Bullitt fuel door