Timing could be off, valves may need to be adjusted, you may need to clean the carb better. Did you make sure EVERY little passage was clear, how did the gaskets and diaphragms look? You might also check the coil wire for damage and make sure it has good contact with the plug boot. Also, check for any damaged or loose wiring in the ignition system, this includes any switches. Lastly, there are some direct resistance tests you can do to check the ignition components using a multimeter. If you don't have a repair manual, I would strongly recommend getting one, it will have all of the specs for the ignition tests as well as valve clearances and other critical info you will need to properly maintain your machine.
Yours truly, sincerelly, love always, Josh aka The DirtDemon.