Non similar bike but i had a cannondale that would not run right when hot. Ran fine for short trips then the throttle would be goofy for lack of a better term.
I ran around replacing coils and such but replacing my tps fixed my issue. I think setting your idle to stock and syncing your tps would be a good start. You can check the resistance of your tps with an ohm meter and see if there is a spot where its value drops significantly.
Hope you figure it out.