i just went through this this week. Started at zero with the cap on , removed the cap, 004". pulled it all apart. measured the thickness of the thrust surfaces, they vaire .002". sand the bearing with 1000 grit on a piece o glass, pushing harder on the thick area's. Now everything measures even. Reinstall all parts loose, hit crank with a soft ace back and forth, .004". Screw the studs in, no binding. Tighten the cap, .002". The only thing I can think is the thrust surfaces are not 90 degrees to the crank. I know the side of the cap is because I ground them when I line honed it at 90 to the cap register. I couldn't grind the inner surface where the thrust sets. Bottom line: It ran 300 passes this way and the old thrust bearing looked fine. I started with .002" last time, but when I took it apart it had worked to .006', knocking off the high spots. My 2 Cents. . Just unassembled the short block, side clearance to tight. The new rods are dead on the money but the old crank is tighter than I like. Now i'm waiting for the new rods to be ground for side clearance. This thing has fought me every step of the way, it better be faster or I'm taking up Golf.
Doug