When I looked at the specs on the tractor they said it should have 9.5 x 24 size rear tires, and in looking they are indeed that size.
So I guess the only option here would be to modify the fender mount like you suggested.
My thought was to leave the one bottom back bolt in the fender ROPS mount and rotate the fender to the rear of the tractor a little that would possibly give me the room I need and then redrill the fender and rebolt the other three fender mounting bolts.
But that was my first thought I'll give it a bit more eye balling and think on it. In raising the fender one must consider that the ROPS bar is formed to the fender contour and there fore to raise the fender one must notch the fender to allow the fender to slide upward.