How is the idle? Does it idle really high and the idle screw does nothing? I know I had similar issues when i was leaking air at the head gasket. Ran great until warm then it was a slug off the line to about 15-20 then the power kicked back in.
Run the bike and check for airleaks by spraying carb cleaner around your head gasket and intake manifold. If the bike dies then you have an airleak.
You should really put your stock carb and air filter back on and start trouble shooting from there.