Welcome to the wonder world of AC bearing fitting.
You can plasticguage those bearings till your blue in the face and the crank will still bind up when you tighten up all the main caps.
All the old WCs,WDs etc that come in for overhaul now get the block sent straight to the machine shop for a line bore and rods sent in to be resized.
A set of precision bearings then fit properly and no shims are needed.
The time I had to spend (& bill for) fitting those bearings is more then saved by the cost of the line bore and resizing of the rods.
If your stuck putting it together with shims you'll just have to keep moving shims around until you finally compensate for the main bearing bore missalignment.
Trouble is oil pressure suffers from the extra clearance.
Take your time and eventually you'll get it.