If you run one or the other do they still stop after 3 minutes? Do they work every time you start the car from cold? Do they work for a few minutes after sitting idle for a while?
Check your grounds. They may use the same one.
Check all of the circuit breakers as well. When components use just a little bit too much current, they tend to act like a timer. Sometimes GM forgets to tell you that they changed something.
I am assuming that you did not do anything to the wipers, and that they worked properly before the AC rebuild. If that is so, I would suspect the AC system. You could disconnect the AC parts, and see if the wipers still act up. Did you replace the AC compressor clutch?
I do not have the FSM for a 95, so I cannot help you a lot with the trouble shooting.