Well the good news is, providing the parts you have replaced are in good order, you have changed just about anything it could be.
The bad news is now you have to find what is actually wrong. The symptoms you are showing suggest that there is a problem with airflow, fuelling or ignition.
Stupid question first - is the throttle cable adjusted so that the throttle fully opens? Basic I know but that's the start point.
Then: Have you checked the valve clearances?
Are the plugs clean and set correctly?
I am also assuming the bike does not rev in all gears and also when it is not in gear?
Assuming the above is ok:
In my opinion, which rarely is correct
as you say the bike is fine until it gets warm it strongly suggests that there is insufficent fuel getting through. i.e. when the bike is cold the 'choke' allows more fuel / less air in, once it warms up the mixture is weakened - as you say this is when you have a problem then it points to this being the issue. i.e. lack of fuel.
If the fuel pipes / filter are clear and unblocked and there are no leaks from vacuum hoses etc. then I would be looking at the injectors.
Can't in all honesty - unless the bike has VERY high mileage, see it being anything else. Would like to get feedback on how you get on