same thing happened with my 99.5...
my 99.5 1.8Tqstip did the exact same thing you are describing. eventually, it would misfire so much that the check engine light came on. (happened 3 times) i took it to the dealer and they just replaced a couple sensors (coolant temp) and my fouled plugs . this did nothing to solve the problem. the issue is that the plugs are building up carbon deposits. i do a TON of city driving, like 90%, and use lots of boost. this creates a lot of unburned fuel, and hence, the carbon deposits. go to your local auto parts store and pick a fuel system cleaner. i did this and my car has run MUCH better since, although not perfectly. get one to reduce carbon deposits. good luck, and i hope this helps.