First step would be to check and make sure that it has had the ground fix performed. Honda powder coated the grounding points where the harness grounds to the frame by the coils. Need to pull those grounds and file the powder coat off and clean the contacts. What do the plugs look like when you pull them? Is it burning lean? If there have been extensive mods to the airbox and exhaust, you may also need a fuel manager. When I changed my mufflers I had a problem with hesitation and surging. I got a Cobra FI200R, with the factory harness connectors rather than the wire taps. It took care of my mixture problems by enrichening the low rpm mixture. I left the mid-range and upper RPM mixture alone.