I have an 06 250ex and I just put a wiseco top end in it. I've got about 3 hours on the rebuild and since the first start up if it cuts off hot it is hard to restart. Normally I would assume the valve lash was to tight, or the carb wasn't adjusted right, however I adjusted the valves myself with a .005" (.127mm) gauge, leaving them a hair loose, and the carb was spot on before the rebuild. I'm guessing it's an electrical problem, CDI or coil. Here are the symptoms: randomly cut out cold at hot idle, may restart with ease may have to sit for 15 minutes, after restart it may cut out at about 2000-2500rpm then run with out a problem, and when it usually cuts out at idle it doesn't skip or pop most of the time it just dies like you cut it off. Any input or suggestions on things to check is greatly appreciated.

 

Based on your description, I agree that it does sound like an electrical issue, especially since you said it ran fine before the top end job. I experienced a similar issue with an 85 ATC250R. I replace the spark plug, ignition switch, coil, cdi, rectifier and stator. Fortunately I had bought all of these used for a really good price to have as spares. I'll be damned if it wasn't a loose connection! Start with the easiest first, which is probable changing the spark plug, then check you connections, or vis versa, and go from there. I hate electrical problems. Especially since the last one was so simple and it made a total *** out of me.

 

The spark plug is relatively new, however I have a lower cost "hotter" coil so I'm going to put the OE coil back on and see if it fixes the problem.

 

Putting the OE coil back on fixed the problem.

 

Outstanding. Glad you got it figured out.