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Sounds like you might have some air in the system. As you sit on the bike, on the right hand top of the radiator, there is a bleed screw that will allow you to 'burp" the air out of the system. I would try that to see if the system has some air trapped in it.
The warning lights typically take 3 complete warm-up and cool-down cycles before they go out and even after that the codes that they generate remain in the ECM for a long time (can't remember the total number of heat cycles it takes before the codes completely clear out of the ECM). The only way to completely get rid of the codes is to connect and OBD2 compliant data tool to the bike and clear the codes.
Best way to be sure what's going on would be to take the bike to your dealer and have them diagnose the problem.
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