^ Not ruling it out.
The symptoms Aaron is describing I have seen before with two different ignitions on the same bike. The ignitions ran properly on a different 250 however. These were race bikes but I was letting them play with the non programmables. The racer who had issues would get the bike to start and would have the symptoms that Aaron is describing. When completely hot the engine would not exhibit any issues. When cold it would act up. She went in and checked the valves and she was not at 7500 miles yet either. She found not only were her valves a little tight but the motor was just slightly off TDC as well. Once everything was in order we threw her new ignition on and she has yet to have an issue.
I have a fleet of bikes to test it on out here if it doesn't work properly there. As said if theres an issue I will handle it