i used to think there was a rev limiter too. until i started tuning the carb and cleaned out the exhaust.
my QT50 with stock gears, stock exhaust, stock head, stock stock stock, properly jetted carb, premixed 50:1 with amsoil interceptor and a few holes in the airbox will hit 38mph downhill. down even a slight hill its up over 30 for sure. cruise the flats at 28-29 all day long and i weigh 185. if i tuck i can get a little more.
i have a bike computer calibrated as close as i can get it so these arent bogus speeds im posting. if anything you're probably going slower than 25. when i first got my QT it would only do about 22-23 and suffered from all the symptoms you are having.
there is NO 'limiter' in the sense that at a certain RPM the spark cuts out completely or gas flow suddenly cant keep up. you are either improperly jetted, or your carb cant get enough gas to it because something is clogged. when everything is working right the bowl can easily fill fast enough to keep up with 38mph.
you are probably suffering from a little of both. do you have a fuel filter in the gas line? if not, i doubt the carb is super clean any more...
as for the CDI, you didnt need to cut it open. the schematic for the CDI is floating around on this site. use search feature. there is an RC timing circuit that controls the advance a bit, but its not a cutout by any means.
as for YT/YF parts, ive posted everything you need to know about the 60cc upgrade including the cheapest source for them (unless you want to gamble with used parts off ebay), along with lots of other tips on the QT at the end of this thread:
so before you do anything drastic, reclean the entire fuel system including the vents in the gas cap, install a fuel filter, burn out the exhaust and check the exhaust port for carbon when the pipe is off, and drill holes in the airbox as described in the above link. if it were me, i wouldnt spend any money on the 60cc upgrade until i knew i could tune it with 50 cc's to match my above stated performance just so you know the engine is good.
hey karl, you got a PW gear running yet??