Yeah, everything I look at just puts me right back at the Ford 44 rotors, and grinding down the axle flanges as you describe. Unfortunately that means I have to wait for the axle to be installed before I can build my brakes. I wanted to have the axles all complete and ready to go before I started building the suspension.
Can you rig something up that will spin the axles on a bearing for you? Build a quick little crank handle with some spare tube and have somebody spin the pinion fast and steady while you grind.