Any possibility that your engine control electronics are getting whacked out and are really putting a very bad or inconsistent timing advance curve to the engine. Bad temperature sender,bad ambient temperature sender,bad R.P.M. information being sent to control module. With your electronics on board, could be sensors or the wiring, or the control unit itself, but when you get engine back together, check the basics, especially if what your are reading about your timing is accurate.
As for as mechanical noise, the first thing that came to my mind was something in the valve train. Second thing that come to mind would be proper piston clearance and ring gap if using hypo pistons. Is cam truly installed straight up and not advanced?
I would do a compression test, would be interested in what it pumps!