Update 4: Until it started thumping again. However, it definitely seemed like it was more forward and it was more infrequent. I decided to change the spark plugs and clean the TB while I was in there since that is what the dealer was going to do next (but not under warranty since the plugs are not covered) and that was a tedious but not overly difficult job. I did myself a favor and after fighting those two clamps at the back of the engine bay I went and bought one of those hose clamp tools. Totally worth the $35! Got both off in about 10 seconds after fighting them for about 30 minutes.
I got the spark plugs removed and 2 of them were gapped at .055, one was at .060, two were at .072, and one was at .085! So that might have been causing some of my misfire issues since that is now what I think was the leftover problem. She's running good today and I'm a happy camper!