Recently I changed my CCT's to manuals and when removing the one on the rear cylinder it slipped meaning i had to reset the cams. Well I managed to rock up basically and set the 180o out. Meaning when it was ridden:
- It sounded boomy/hollow
Revved / revs to 7k then stops like it's hit a limiter (about 100mph)
Keeps stopping/almost stalling then carrying on at idle / low RPM. Disconcerting noise.
Runs much better now but still makes the weird stopping thing when idleing. It's been dynojetted so i'll put it down to that. Also while you're there, take the covers off the cam chain and set the tension on properly (if you have manual CCTs). There's some confusion about this due to a misprint on the APE CCT instructions. Basically you should have 6mm TOTAL SLACK (NOT DEFLECTION!!) between the cams. This means 3mm each way from it's resting position. That's 3mm deflection, 6mm slack, not 6mm deflection as originally stated.

Hopefully that might help someone who's had some problems.
(P.S I think that's the right procedure (was a while ago now), worked for me anyway. If you would like to make any amendments, let me know).