Hooksey
I don't have a 750 to look at, but just trying to make sense of the info submitted so far.
1. Brad has 2.5mm clearance between the end of the crank and the inside of the cover, and his shaft protrudes 1mm beyond the nut. So there is 3.5mm clearance between the nut and the cover.
2. Your shaft doesn't protrude beyond the nut.
3. JLO has 56mm from the cover mating face to the end of the crank.
4. You have 60mm to the end of the crank.
5. Your crankshaft pulley is in the correct position on the tapered shaft (your and JLO's 40mm measurements match)
Considering all of the above, a likely conclusion is that someone has installed a non-standard nut on your crankshaft, or a non-standard washer behind it. Before you filed it down, your nut/washer combo appears to have been 4mm thicker than it should be (JLO's 60mm minus your 56mm). Filing 0.5mm off it brings its "over-thickness" dimension back to 3.5mm, which gives zero clearance inside the cover (see point 1 above). But the fraction of a millimeter that your nut has already milled off the inside of the cover actually gives you a bit of clearance. If you want to give it a bit more room, get a thinner washer or take off another millimeter or two off the nut.
It would be interesting to confirm all this speculation by having you guys measure your nuts
Cheers,
Cam