This has to be one of the simplest, most effective how-to's I have come across. I was ready to cut slits in my fender, bend and reweld it when I found this how-to by Raz on the JockeyJournal. Radius your motorcycle rear fender to fit your wheels just right with some scrap 2"x4"s.
So here's what I do to remedy the fit. Lay the fender on the bench, get some 2"x4"s and place the ends of the 2"x4"s on the rolled edge of the fender (if the fender dos not have a rolled edge I don't think this will work as well).
Apply some pressure to the other end of the 2"x4"s, this will push the skirts apart as the fender gets wider the radius will shrink.
Work from one end of the fender to the other moving the 2"x4"s in 3" - 4" increments.
After you have gone from one end to the other check the fit on the tire.........it's not quite there yet.
So repeat the process again this time pushing the end of the 2"x4"s closer together (or increasing the size of the wood block between them), then check the fit again.