I have 245/75R16 M/Ts (30.7x9.8", specifically) on stock 2003 Limited rims. I used to have rubbing on the swaybar, fog light doors, rear flares (door area), and also in the rear on the upper body exposed from removing my wheel well liners. I got 1.25" wheel spacers and that seems to have solved most of it along with removing the liners. I still have a little rub on the lower horizontal lip of the rear flares where the lining used to connect to the flare. I know if I spent 10 minutes with the flares off and put my dremel to use I'd be an easy fix.
A little OT, but...
I've thought about cutting that lip/edge from all the flares to try and clear 31x10.5" Interco LTBs. I don't think it would look too bad

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2003 Limited, Silver - L.O.S.T. # 068957 Rockies
http://www.cardomain.com/ride/2127390/14
2006 Kawasaki KLR650