Once the engine is warm and stopped running, if you let it sit for another 15 minutes (not long enough to cool completely), will it demonstrate the same problem? If so, you may have a partially blocked fuel line, petcock, fuel filter, or tank breather. This problem would appear every 15 minutes regardless whether warm or cold, although the 15 minues may be reduced if you're using the choke to warm it up.
If it really is temperature related, it could possibly be electrical. As a very general statement, electronics prefer colder temperatures to warmr ones. Do you have a friend with asimilar machine that you could swap electrical parts with?
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2004 Yamaha YFZ450
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