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My wife has a '00 Jetta, same motor.I tend to think the water just brought to the surface an already existing issue. I'm guessing relatively high miles and no/unknown history on plugs,wires,and coil. If thats the case replace all 3. Important---use VW wires and coil, don't cheap out. My wifes car had similar symptoms, turns out mpg's had been decreasing for awhile and power went down gradually, driving everyday she didn't notice, but driving it infrequently I noticed it was real slow. Within a week the CEL came on & it started misfiring noticeably.
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