pavement blues

I have not been on my bike since last July due to injury. During this layoff I reinstalled all of the dual sport equipment and had to make new wiring harnesses. I had ripped out all of the extraneous wiring after deciding not to ride on the street again. Well, never say never.
After recuperating enough to throw a leg over the bike I took it out for a short trail ride on a 20 mile loop with 5 miles of street on the way home. It ran fine on the trails ( I rode slow) but when I got out on the pavement it began to misfire, lose power, and backfire after about 1 mile. I limped it home. Since I had installed a new Iridium plug and adjusted the valves before the ride I changed back to a standard C8E and re-adjusted the valves. I took it out again and the same thing happened. It ran great until sustained pavement driving and exhibited the same symptoms again.
I have checked the gas cap vent, disassembled the carb and checked for dirt or obstructions, checked fuel flow from the petcock, the spark is nice and blue, and all electrical connections are tight. This week-end we will drain the tank and refill with fresh fuel, check the fuel transfer pump, and ??.
Any suggestions? Yeah I know.. buy an '05, but what am I missing here?
Dez

Thanks, that seems most logical and will go to the top of the list of potential fixes. 'preciate the help.
Dez