Sometimes best to have a fresh pair of eyes on it, bounce some ideas about. Bloody difficult to sit here and guess the problem.

Valve gap (checking clearance) was mentioned above by gingerturbo... tbh though,I'd expect any valve problem (if leaking) to be picked up on a compression test.

I'd go back to basics, check the cam - crank timing, check the valve clearances , make sure the exhaust isn't blocked, make sure it's getting full throttle, that sort of thing and go from there.

Does it actually misfire/stutter when driving or just feel restricted?

In the meantime, I need some help with a Focus 1.6 TDCI diesel that's as flat as a witches tit.