You know I think this could well be timing related.(Something I say VERY rarely) If this is as well as its ever run the timing cannot be discounted. (pun intended)I don't think its anything silly like the woodruf key, I think it may just have been done wrong.
It needs be out by little more than a couple of mm and it will run but any revs will advance it passed the point of not running.
1.8mm BTDC for your bike , do you have a puller and a dial gauge, you don't have to have the dial gauge but the puller is a must.