Is the hesitation felt when you have some throttle on, like when accelerating, or just cruising at light throttle?
One thing you didn't mention is checking the throttle body rubber boots. A known problem, they are very prone to coming loose after a backfire. This allows unmetered air into the engine and causes all kinds of fueling issues. You might have to pull the tank to inspect them properly. You can get by with reseating them and tightening the clamps better, some go further with the fix for it. Checking them is good for now. If your throttle bodies are properly synched, tps bar is raising around 1700-1800 rpm, and the secondary throttle plates are not too far off you might still get an occasional hiccup but nothing like you are describing.
If you are feeling this as you accelerate it could be the clutch basket. While the engine isn't misfiring, I have had many owners say that is what it feels like. While riding through the 2500-4000 rpm range gently feather the clutch lever. Not so much the clutch slips, just enough to load the pressure plate a bit. If this smooths out the engine significantly, you can bet the clutch basket is worn.
While I am not usually a believer in engine treatments, I do have some faith in Sea Foam fuel system cleaner. On the off chance you have an injector not firing well, there is a chance the Sea Foam will clean it up a bit. It won't hurt anything at any rate.