I own a 2001 TT 1.8 I had somewhat the same problem. It seems that our Gernman engineering isnt all's it chracked up to be. I too continued to have multiple misfires and since I took care of the inferior wiring installed on my TT not a problem since. Take a look at the wiring to the spark plug coils each one of mine had broken insulation. Ive worked aircraft electrical systems my whole life and curent take the path of least resistance. I found that due to the heat generated from the engine the insulation breaks down, upon removing the tape wrapped around the wire harness the insulation wahs broke or had shrunk in numerous places. Directly behind the coil plug I found the center conductor (wire) exposed to the point it shrted to the valve cove or even worse than that to the other wires that had exposed wire. I bought some 18 gage high temp wire and used enviromental splices removing the bad wire as far down the harness as possible, replacing the wire one wire at a time. Some of the breaks were very close to the plug its self when I repaired them I only cut the wire to the point of the inuslation break and installed just a splice. After you get the bad wiring replaced string tie the wires dont wrap them and then install convoluted tubing. (black tube you can buy at any auto store) some come with a slice on one side so you can install the wires if its not lay it long wise on your bench take a razor knife or somthing like it slice it and install it on the harness only the plugs for the coil shoud come out for each cyclinder. This took all of maybe 45 minutes. Since the repair no misfires no engine lights.