I would be looking at the reeds and main jet. Main jet would be easy to check for debris without much disassembly. I was told that the reeds only affect bottom end before, but from experience, I found that with broken petals the bike started, but would not rev. More throttle equaled more bog. I'm confused a little that you say that you shut off the gas to run it out of gas and are surprised it revs before it dies. Not sure about that method helping with longevity either.
You should always know if it starts revving off of idle for no reason, the carb is out of fuel and the air/fuel mixture is leaning out causing a rev. Sometimes you forget to turn the gas on after a break, or just plain run out of gas, even a clogged petcock with a slow flow acts like that. It can Braaaaaaaaap, and take off like a rocket with just a little throttle when its almost out of gas. Scary on a 500.
No power at the top-end is not related to that. You called it probably, when you said it happens when the main should open. I blow through main jets onto a piece of paper to analyze what got in there and how. Is it smoking like a mosquito fogger when this happens? If so, could be crank seals. Good Luck.