ok, ive had that topend, and overall its pretty good. the cy 36mm topends are pretty good, but the 35mm ones are poop, all of them.
you probably have a bit of heat soaking going on. earlier, did it seem to lose topend power (before it was "missing")? the more you ran, the more the topend suffered? if yes, you were seeing heat soaking, which is a condition of to high of a compression, which can be one of the main quirks with this topend in stock form. they are around 17:1 maybe 17.5:1 compression which is high. You can try High Octane fuel (100 and up) which may help. but you ll likely need to raise the cylinder a bit. i would use a cooper .025 cylinder gasket. the .005 extra clearance will lower compression a smidge, and shoudl help eliminate the heat soaking.
but you have a 2ndary condition of the heat soaking (which is running hot basically). the heat has probaly weakened the oil seals as you noted. and likely hurt the bearings in the process. this is only a theroy i have, but i think it plays out pretty close to the actaul sequence of events.
the motor gets hot.
the heat plays hell on the oil seals and bearings.
over time, the seals weaking.
part of the motor process of high rpm, is high case pressure.
the higher case pressure, pushing agains the now weakened oil seal, blows by the oil seal.
the sudden release in case pressure at high rpm, caused the motor to miss.
often you can hear a loud "Popping" noise when this happens. i suspect this is the oil seals slapping back against the crank after the case pressure (large burst of high pressure heated gasses) push past the weakened seals.
just a theroy as i noted, but i think its pretty sound.
fix is new case bearings, and oil seals. install a .025 copper cylinder gasket. when you take the cylinder off, check over the cylinder walls very well. see that its still good.
i would also replace the wrist pin bearing as well as the ring while your there. and ofcourse the other gaskets, ie, case, carb, exhaust ect...