Volkswagen Repair: 2000 Beetle Electrical and alarm problems, haynes repair manual, door latch

Question
I recently purchased a used 2000 Beetle. GLX 2.0L. Automatic. It has 109,000 miles on it. Had it to a mechanic that was recommended to me as electrical expert (not VW dealer as it is not under warranty). The first problem was the AC had stopped being cold and the mechanic said one of the AC fans blew a fuse. They replaced fan, AC compressor and fuse, and the AC now works. The interior lights would not go on when door opened. The mechanic took out light in door panel that was damaged to see if this was part of problem. They told me the lighting problem was due to the door latch sticking, as the car had recently been repainted. Lights still did not work. When I got the car back, windows would not go down and sunroof would not open. I took it back and they said the damaged door light wires were touching and caused a short. They then fixed this. I have had a problem on 2 occasions, both prior to and now after that repair, not being able to disarm the alarm system. This latest problem with alarm system did happen today after a heavy rain, and also just after I had the upholstery replaced on the doors last week. The alarm started going off for no reason. It sounds for about a minute and goes off by itself. I'm able to start the car and go with the alarm sounding. The doors do have buttons that go up and down to show locked or unlocked, and a red light that blinks when the alarm is armed. When the alarm is working properly, the light does not blink when the door is unlocked with a key. When the alarm is malfunctioning, this light blinks all the time, even when door is open, and when I close the door and lock it, it does not beep to show I've armed the alarm like it should. Also, the interior lights are now not going on again when you open the door, but they do come on for a brief period when I turn the car off. Do any or several of these problems relate to the comfort control module and if so, what can we do? From the Haynes Repair manual, it looks like fuse numbers 111 and 144 are alarm system fuses. Where are they located and if you pull these fuses, would this solve the alarm going off until I can get it fixed? Also, 144 is also central locking. If I remove this, will I be unable to unlock the passenger door (passenger door has no key entry)? Thank you very much for your excellent service and please let me know if I can provide any other information.

Answer
Hi Clark;
Even in the early "New Beetles" the electrical systems are different than those found in ANY other cars.  I'm sorry to hear that you took the car to a repair facility that doesn't know VW's very well.  His explanations are crap, for what has happened to the electrical system in the drivers door is related to BOTH the door latch, and the window motor(which is where the "comfort module" is located).  The comfort module is the part that communicates with the door latch, and the alarm.  The Haynes manual is not a very good source of information.  Get the "Bentley's" to get a better idea of the car, and how to repair it.
It sound to me like the window motor, and the door latch both need to be replaced.  Do not take it back to the place that got you to this position.  The parts are expensive, so do what you can to live with the situation for now, and save for the parts, and buy them at the dealer, if they are not the right ones there is some recourse when dealing face to face, but not off of the Internet.  You can then replace them yourself, or at the dealer, your choice.  There is, I expect, some damage to the wiring in the drivers door now, due to the "repairs" from the other shop.  You should ask your VW dealer to let you know what they find, at least.  That way you'll know what's going on when something else starts acting funny in the future.  I'm sorry for your trouble, Clark.  I hope some of this information helps a little.