TPS and carb balancing has a big effect at small throttle openings, getting them right makes the bike much smoother at low speeds... not much effect higher up the rev range though.
A new air filter might help. How many miles does it have on it?
I've a pet theory that the carb slides start to lose their teflon coating by about 50,000 miles. This means they can jam if the throttle is opened suddenly causing the bike to bog down, but if the throttle is opened gently the slide has more of a chance to move before the vacuum causes it to stick. Really need to poke a camera into the airbox to see if this explanation holds water though.