Just wanted to say that the main bolts are tightened dry. Lubrication would cause false torque values in this case. Also here are the piston protrusion measurements for all AAZ head gasket thicknesses.
0.66 - 0.86 mm: 1 notch
0.87 - 0.90 mm: 2 notch
0.91 - 1.02 mm: 3 notch
I'd also recommend adding some filler around the deformed area of the crank sprocket to support near the ends of the D flat; the distorted area might rub flat after a while. Just a paranoid man's bit of advice.
As for the main bearing concern, t might be time to check the alignment of your main journals, assuming you actually used some oil or assembly lubrication when spinning the crank while the caps were partially tightened. Was this the engine that had had it's journals already over-sized?That might explain the markings due to poor machine work done during the original rebuild. And are you sure you had the main caps aligned correctly? Just asking.