What kind of jeep is this?
The cj and yj had a seperate stand alone ac unit, so the bypass will do no good. if a tj is what you have, you may want to give the info on how you checket the freon level. on the 134a equipped vehicles, a half pound from full will give you fits. also, having the system reclaimed and recharged can sometimes help , due to small ammounts of moisture built up in the system. with that being said, the climate comtrols with vac assist have been problematic for chrysler, jeep and dodge in particular, so that door prob you were refering to may very well be it. if you notice a change in the sound of the fan under acceleration, this may be the culprit, and good luck finding the vac leak, as they usually prove to be illusive.
hope this helps...
Glenn