It sounds like your main jet is clogged. I have found on my own CT3 that was the case when I got it.. The main jet is easy to remove and replace, or if you have something to clean it with, (i use 1 strand of wire from a wire brush), this would be an easy place to start. Do not make the hole any bigger with a drillbit! also check your sparkplug and make sure it is correct as well as the correct gap.
Another culprit could be a dirty or even missing air filter. These are still avail. from Yamaha at your local yamaha dealer.. There is yet another possible place to check, your points. if they points are set incorrectly, or worn this would cause misfire at mid to high R's. Im restoring a ct3 now, and I would be glad to offer any assistance I can. Best of luck!
Breakpoint