Man, I hope recharging does the trick. I don't have the exact same problem of it not 'cranking over' once it's been ridden to hot temps.
I've had 'bogging' problems at higher RPM's (anything over 4-5k). When this first happened in March/April, I bought a new OEM battery, and problem was solved. Now it started the same problem last week, and I charged the battery (yes, the new one), and the problem hasn't come back (but the charger was stating that the battery was good)...but then again, I haven't really gotten on the throttle very hard either (since the problem can buck me off the bike).
So, I've been doing research, and it doesnt SEEM like the rectifier. I'm trying to see if it could possibly be the stator? I was cruising cbrworld, and someone said that the bike is supposed to stay on even after you disconnect the negative terminal (like a car)...which, my bike shuts off right away. ???