Wow, that is really bad news. You changed basicly everything but the crank, and I assume when it was welded and ground it was checked for everything. So, I am thinking something else is the cause.

What bearings are you using?

FWIW, in my 511 low deck I use Clevite MS1277HG main bearings (0.0029") [RB mains],
and Clevite CB-743HXK (xtra clearance, coated, 0.0020") [2.200 journals].
I am not saying you need the coated bearings, that is just what I use, and would run looser (0.0025") without coating. I currently have 529 passes on the rod bearings, and 247 on the mains. The rod bearings always looked like new during the inspections, so I keep putting them back in. The mains were OK at the last inspection, but not perfect so I changed them while it was apart.

I would look real close at the oiling system also.
What was the piston to head clearance?