I had this problem on my 2002 passat. it was the ignition coils. first set were replaced in 2002 as a vw recall. second set (at 122K miles) were relatively inexpensive to fix. just one failed but it made the engine run really rough - my mechanic was able to move it from one cylinder to the next to get the problem to repeat.
1st thing you must do is have engine trouble codes read. Most parts stores do this for free. They will plug a hand held scanner into the vw's diagnostic port (usually located under the dash) and will 'read' any trouble codes stored in the cars computer (which have caused the check engine light to flash), They will explain what the codes mean and offer advice, write down the codes, and if you have any further questions, post the codes and questions here.
good luck!
Change the spark plugs and the weirs, you need a tune up it cost $350 but you can do it, its easy
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I have the same Problem. My car is v6 and has also loss a lot o power an shakes so roughly.
I have random cilinder misfire. It started out just under load, but now it happens after a few minutes of warm up. I changed plug/wires/coil/fuel filter/air filter...What could this be. it runs well for a short time, then power loss and shaking engine. I have a code reader, and it says misfire in random cilinders.
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