I'm posting this hoping it will help someone.
I had a misfire at idle, not very noticeable, no SES light. At 2k rpms in 2nd gear or above the engine would stumble. At 3k+ rpms it would even out and feel fine but not quite as much power as it should have. Pulling codes with INPA showed "A" misfire on exhaust side for cylinders 1,2,3,5 and 6 at 640rpms regularly. Eventually it registered a misfire with "cat damage",Digiprog III or kat damage, around 4k rpms which triggered the SES light and eventually limp mode.
Checked the INPA Run Unrest page, It showed cylinder 3 over 1000, other cylinders also showed very high but not over 1000.
Checked the spark plugs, they were 2-3 years old, maybe 40k on them, nothing stood out. Went ahead and replaced them. No change.
Purchased an ignition coil from advanced auto, carquest if that matters, for testing purposes, fits, but clamp doesn't fit. Bremi on order.
Replaced cylinder 3 ignition coil, no change, cylinder 1, no change, 5 no change.
Finally replaced the cylinder 6 ignition coil,Vagcom 15.7 and the misfire is gone along with the high Run Unrest numbers across the board.
I searched on the board and saw some others with similar issues but theirs either pointed directly to the culprit or did in a round about way. I don't think mine showed any indication of being cylinder 6 as the culprit. I think the lesson here is, check them all.