Well that can be a tough one. I can give you some examples but I cannot guarantee any of those is the problem you are facing:
-Fuel pump suction hose within the fuel tank is loose. (maybe you noticed that this happens more so when you have 1/4 tank or less?)
-bad front (pre cat) lambda (also known as o2/oxygen) sensors can cause idle or general RPM surging.
-a very dirty/bad MAF can contribute to surging as well
-Vacuum hoses
-Throttle Body and intake hose
-of course bad coil packs and spark plugs

These are just some of the things I can think of off the top of my head. Most of them should throw some kind of soft code (only readable with a vagcom, generic OBD2 will not see those). You should check if anyone you know or someone in the area (from a forum) would be willing to hook up his Vag and read your internal codes (the ones that don't throw a CEL yet).

 

Thanks for the help Jim.
Scott

 

I just had the coils checked and coil "g" was replaced since it was faulty. As for the surge, I added a can of Seafoam to the fuel tank and now it's running better than before. Since then, my worn brake pads light has come on. In terms of replacement, what do you guys recommend. Are the EBC RedStuff pads a good choice?