Have you checked the clearance with plastigage? It sounds like there is a high spot somewhere or the crank wasn't turned enough. As Jerry said you can use Prussian Blue to tell you where that high spot is. Did you check the crank to see if it was straight when you had it turned? A bent crank will do the same thing.
You'll have dowel pins in the bearing caps. These fit into the recessed holes in the bearing caps. You should only have dowel pins between the cap and the block in the rear main cap...
One other thought...and this is really a long shot...but make certain there isn't anything in the recessed hole of the bearing cap or stuck to the bearing surface of the bearing cap or the back side of the bearing itself (like a sticker) that would be causing your bearing insert to be pressed against the crank journal.
Jon


~ Jon
1952 1/2 ton with 1959 235 | T5 with 3.07 rear end