I haven't had a misfire since I cleared the codes weeks ago. Clearing the codes didn't fix it, that just fixed the light. The car seems to have fixed itself.
Checking the coil packs is a great idea but it doesn't appear to be necessary. Thanks for the suggestions.
Prayers to the most high for our cars fixing itself... my GTI 2.0T had a misfire on cylinder 2, I inspected the spark plug, nothing wrong, it looks clean, I swapped the ignition coils around (R8 ignition coils) to see if it's the ignition coils, no mis-fires yet, nothing crazy to trigger a code.
I was told the 2.0TSI has NORMAL slight misfires (which my scanning tool picks up, just a couple misfires on all 4 cylinders). Which is apparently normal... I just don't check anymore and I drive it without thinking too much about it.
I did notice a little tiny amount of oil around the thread of the spark plugs... yes.. time for head valve cover gasket replacement but all the shops said to push it off, it's not that bad yet so I'm listening to the shops.