Just a thought (and dont think you mentioned it....)
You said that you have had the flywheel lightened, have you had it balanced to the rotating parts?
Its a bit of a long shot but (and this is assuming you havent unbolted the knock sensor already) if the knock sensor is seeing frequences it doesnt like, it could start playing with timing and possibly fuel trims(?). Also, you said you have had 3mm skimmed from the head. It sounds like a lot. Do you know your CR (compression ratio) as this may also confuse the ecus knock sensor readings.
* Just noticed 'Arc' already mentioned knock sensor stuff!!! *
I would be tempted to also try a different ecu if thats feasable. At one point I was looking at using a p75 ecu but got stuck at the time trying to get it 'decoded'.
Are the injectors the same ballpark resistance that the ecu is expecting
Im just clutching at straws and writing stuff down as I think of it......