Alright, I ran a can of Sea Foam Engine Tune through the engine, and it magically self healed. I am good with that. I still am going to put and crank in it to make sure it doesn't start knocking again. This thing has been such a roller coaster of emotions.
It's also kind of funny, parked in the shop, it runs great and doesn't miss, but take it out on the road and it starts missing.