Do you have fuel-filter between tank and carbs?
Pull carbs and inspect float-bowls really carefully. I've found all sorts of debris that cause exact same symptoms as you. Works for a while, then floating debris gets sucked up and clogs end of main-jet. Let sit for while, debris falls off and bike runs fine for awhile. Until debris is sucked up yet again.
I found this critter in one of my pre-gen carbs...
