Answers: Okay, I would take a look underneath the hood and see if any hoses are loose. If any of the turbo piping came loose, that would explain the extra clamour and the extreme loss of power. That would be the first thing to check. If you look it over really apposite and don't see any visible problems, transport it into the dealership, because I have no belief. Let me know what you see...my brother has one of those, so if you can explain to me the area the resonance is coming from under the hood, I might be capable of help you. Good luck!
The muffler wouldn't affect the loss of power. You could involve a tune-up, check your oil. If it's a 2003 it might still be beneath warranty. My 2005 Jetta had a 5 year warranty.
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