Volkswagen Jetta Questions

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I have a 2002 VW Jetta with 201,500 miles. I was having an issue with the car running rough, and then finally the blinking check engine light came on and I had it towed to the shop. The shop replaced the spark plugs and wires (a 'tune up') and the car ran better.

However, I now have a NEW PROBLEM where the car will run rough on occasion. Sometimes I will go to start the car and it will run OK, but pretty rough, and then when I come into a stop light and the car comes to a complete stop, it will 'jump' repeatedly - any idling is difficult for the car.

Then one morning I went out and it just would not run hardly at all. It was extremely, extremely rough. I had it towed again. My mechanic looked at it the next morning and said it ran a little rough going into the shop, but he cleared the two codes (cat. converter & engine misfire) and it ran perfectly fine after that.

I have had the car back now for about 1 week since last bringing to mechanic and it has ran fine excepting one time, and that was after it rained. I can't definitively say yes/no to a pattern (of running rough & rain), but it has been true at least since I have been paying attention to it.

My thoughts are that when the mechanic did the tuneup, maybe he cracked a plastic component that houses an electrical part? I have also been researching the issue and it seems I should check the ignition coils for problems, but I do not know how to do that and don't really want to keep bringing the car to my mechanic and having him $$ me for no answers!
I checked the fuse box from under the hood and inside the car but they all look ok..
My Jetter will not idle with out me pushing in on the accelerator a little. Could this be a result of a faulty throttle position sensor? Also on acceleration the engine will hasitate but smooth out as long as I don't give it to much gas. It is a 5 speed standard transmission and this lose of power is happening through the gear change. Thanks for your help.
when cables disconnected sided to side is fine. Working dampening weight up and down under hood is stiff (problem internal?)
My alternator went out, we had it replaced and my stereo stopped working as well as my clock and odometer looses it's memory after turning the engine off. My needles do not go back down to zero after shutting the car off either.
windshield wiper still displays even though there is no problem ac still blowing out cool air even though compressor is running
Also i noticeced when it hot out side my car makes this loud whistling sound coming from the engine also when i make turns or driving for a period of time. It starts to shake at acceleration poor fuel range . What do i do?
It turns over and starts up but cuts off. Electrical problem?
This occurred twice in one day then while driving on the freeway the engine down shifted from 75 to 65. I was not able to accelerate beyond 65. Occasionally, my EPC light will come on.
Will replacing the Engine Power Control Module resolve or help this problem?
valves and turbo replaced
Powered Door locks for both rear doors fail to lock by key or button on alarm FOB. I can sometime hear something in the doors move when the lock is initiated , but nothing happens. The locks also cannot be activated manually.
Vehicle is throwing a Gross Oil Leak Code.
it js suddenly appeared after hving battery problems
Manufacturer specific code
transmission fluid is in coolant system.
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