Not getting enough fuel or air flow. Once you go past half throttle the bike begins starving (sputtering). Not reving past a certain RPM is typically indicative of a fouled plug, which is itself a symptom of a problem and not the cause.
Given that you've admitted to having electrical issues with the pump wires, an in-line fuel filter, and modified air box, I would say you've narrowed down the trouble areas. Me personally, I'd focus on that bridge at the pump wires. I'm sure Tony can guide you on that one.
NOTE: TPS being slightly off won't cause your issue. My bar was at the top for months before I adjusted it and I never had any problems.