The noise is very disturbing. It sounds like a rod knock. I have seen harness get reversed on engines which causes the timing on 2 cylinders to be waaaay off, and the end result is very unbalanced firing of the engine. You can actually make an engine knock if you feed it the correct misfire. I don't know if this is the case here, but I figured I would ask.
When you had the TMIC off, is there any chance you dropped anything in the throttle body? Were you missing any hardware?
When you took the uppipe loose the second time did the turbo spin free?