I had the same problem when I replaced a rear tire on my 02 boxer. The tire was the right size, belt was aligned/tightened but I didn't have much clearance. At times when I would let off the throttle the lip of the tire would rub the belt...chirp was anoying as hell and the back rim would have black crap all over it.
Not the most technical answer, but I took a dremel tool, put the bike on my cheap motorcycle jack, used a back and forth motion with the dremel on the lip of the tire and rotated the tire removing some of the lip as evenly as possible. IMO, it didn't affect the integrity of the tire and got rid of the chirp. I did this process twice, cuz I was trying to leave as much of the lip as I could get away with. The first time helped a lot and then a few weeks later I duplicated the process and the chirp went away completely.