Update! Hope everyone has had a nice Christmas and has recovered from New Years!
After almost 2000 miles since the engine work, no leaks, only re-torque required was the connection between the header and the rear mini cat.
Engine is running smooth and quiet!
There is still the persistent knocking sound that is only heard from inside the vehicle. It is NOT engine knock. I've monitored the front of the crank to see if the cycle of the knock was the crank moving fore and aft. It is not! I suspect it's a transmission noise. But for now the transmission seams happy! All shifting is normal. Maybe a sticking valve in the shifter pack?