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You've pretty much answered your own question. Either the wastegate is sticking closed or the actuator.
The misfire your feeling is it running extremely lean.
Being a tech really takes it out on your joints doesn't it :( girlfriend made the comment earlier that I sounded like a ratchet with All the clicking I do!
Haha no where near! Did give it a little toe, but yeh I know what you mean, I did my mapping on my ITB'd one there. I was interested to see how yours went as its the spec I will have mine at when I manage to get to pay sharkey!
I've never really made a point of timing it but I thi I my record is just shy of 2 hours on my own car. That was with someone catching the parts as I chucked them at them lol.
Ok good.
Heat marks are usual on a flywheel anyway from everyone I've ever changed. Ask to know the 'run out' of the flywheel and then check yourself if its within tolerance.