Car is back, low RPM miss is gone, weird highway hiccups are gone.
Knock sound still remains as the car shifts. However they've said this is possibly a normal noise. Due to the fact that my damaged cylinder had no deformation at all they suspect the loud noise I was hearing and the small pinging sound were unrelated. They've strongly suggested a tune due to the aftermarket parts.
Aside from possible driveline issues which I would suspect would occur on hard down shifts also which isn't the case.
I can only make this sound occur on steep hills. On flat ground it is non existent.
Will tune and keep everyone posted!