Today I bit the bullet and ground away some of the underside of the upper wing skin and foam core so the tire would fit. I was dreading the job, but it went pretty well (if you don't mind laying on your back sanding over your head with fiberglass dust falling in your face). First I taped some 80 grit to the tire and rotated it against the wing skin to mark where the interference was. Then I used my Dremel to remove a feather-shaped piece of the skin. Next I stuck some 36 grit to the tire and continued working it against the skin to enlarge the area.  When I got close, I placed 3 layers of foam tape under the 36 grit to provide clearance for the 2 bid to be applied later.



Here's the final result of the sanding. The squiggly Sharpie marks are approximately where the edge of the tire was. Inboard is to the right:


With the lower skin (and about half of the foam core) cut away in the required areas, I retracted the gear and it came with the hydraulic cylinder against the stop and the middle gear door perfectly nested into the lower wing skin. Woooo-hoooo! After sanding away the paint for about 1" around the edge of the "wound", I smeared micro into the foam core and applied the 2 bid patch.

I should have put a scale in this photo, but the patch is about 5" x 7"