I have the exact same tire/wheel combo. As you know, these wheels are over an inch further out than stock (-12 offset vs OEM +15), and that creates a larger sweep for the tire, and rubbing against the flares.
All the suggestions above about lifting miss the point that lifting is not really a cure, it's a band aid to avoid rubbing at static conditions, but it won't change suspension travel and it'll still rub under full suspension travel.
It's odd that yours rubs on the rear of the flares, mine rubbed in the front, and only on the passenger side:
For now I just took the bumper flare off, and plan to hit it with a heat gun to deform it slightly.
On our recent offroading trip, where we saw some full articulation, I noticed rubbing against the inside of the wheelwell, at the pinch weld area. Again, I fully expected this when getting the wheels, and am considering the pinch weld mod.
You can always go back to wheels without the negative offset, that'll fix the problem. I specifically wanted the offset to push the tire further out towards the flare, so I'm willing to do the work to eliminate the rubbing.
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1997 4Runner Limited 4WD E-Locker ~200k | Falken Wildpeak A/T3W 265/75/16 | Pro Comp 69 16x8 | OME 2906 | B&M 70264
Addicted Offroad Front Bumper | Spiker Engineering High-Lift Hood Struts and Ultragauge Mount