check your battery with a voltmeter and see what the voltage is. has your bike ever been sitting for any period of time? how old is the battery? is this a 2004 RR? the 03's had a flawed design with the regulator/rectifier but the 04's should have the newer ones. the problem with the old one was that it didn't have a heat shield and it's right by the headers so it'd get extremely hot. there are some troubleshooting diagrams on the net on how to check if your regulator is good or not. i'd charge the battery first and see if that helps.

 

Mine does the same thing. It seemed to start after I had the clutch replaced by th dealer. I replaced the battery and it does the same thing.

 

+1 on the R/R problem, i had the same issue with my '03. when the bike gets hot it doesnt charge the battery or something. also it could be the starter, or a combo. a mechanic said i would probably need to take apart my starter and clean it out because that might have been the problem. some how it just went away, but might start back up again come summer and hot engines.

have you charged the battery on a charger, that could help as well, if its drained charging it will the bike could put strain on the chargeing system (which already seems to have something wrong with it)

take a multi meter to it and see if the if the voltage drops when you try to start it, that should tell you alittle more about the problem, also check the voltage when its running at around 5000 rpms, at hot and normal engine temps.