This might be a difficult one to solve, Firstly, have you got a haynes manual or another manual, that will tell you how to set up the ignition timing, it does however requre a dial test indicator and spark plug adapter to set it to the required 2mm BTDC. I'm a bit confused about this though because you say you checked it with a strobe and it was spot on, so in suspecting the timing you may be barking up the wrong tree. It might be a missfire at 3500/4000 rpm and that could be caused by almost anything, could be
an air leak somewhere
someting blocked or dirty in the carb
faulty CDI
faulty spark plug
worn piston rings / bore
not sure about the air gap you mention, I wouldnt have thought this is an adjustable setting, but if it is then yes maybe its even this, to what extent did you strip and clean the carb if you screw the mixture screw in and out does it have an affect on the idle speed?