Ezzy,
Some things to check / test.
1: battery voltage / charging system. On these bikes low volts can lead to misses. It might be that it's making adequate volts above 6500 revs and that helps it clear up.
2: ground connection loose battery terminals
3: move the coil from the low temp cylinder to another cylinder. If the temp on the new cylinder drops, then it's that coil.
4: bad fuel theory- if it gummed up your throttle bodies / injectors it might be causing the problem. Run a tank of fuel with a cleaner in it. I've had good luck with seafoam or amsoil quickshot
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