I'm in the same boat. There should be enough float in the caliper to handle variations in the thicknesses of everything, and even if you'd goofed up and put the washer inboard of the swingarm, that shouldn't make much of a difference to the brakes. So that blows my error-in-axle-assembly theory out of the water.
I re-read the entire thread to make sure I haven't missed anything, and the only thing that stands out to me is the wear on the inboard pad. The back of the pad should be flat against the side of the caliper body and the front should be parallel to the rotor, and the wear says it isn't. If the outboard pad is fine, the only conclusion I can draw is that the front of the pad isn't seating properly in the caliper. I had a pad that wore the same way (may have even been the same one) once and the cause was improper seating in the cavity. I've installed lots of pads, too, and the rear inboard is the bane of my existence because it's hard to get right.
--Mark