I had exactly that problem with an Olds 455; the cap wasn't cut square when the block was line honed.
I discovered this with feeler gauges; I could get an .008 between cap and crank on the front, but not between block and crank. Knocking the crank to the rear, I could get the feeler gauge between the block and crank, but not the cap and crank. Therefore the cap had to be at an angle.
I filed the parting line of one of the bearing shells--just a touch, and only from oil groove to the rear thrust surface--so as to supply a little more oil to the rear thrust face.
I ran the engine about 35 minutes on a test stand then tore it down for other reasons. It's a classic "long story" that involved a defective lifter and also the garage burning down while the intake manifold was off--and in the end I chose to use another block. The entire rotating assembly went from the first block into the second block; and the thrust bearing looked beautiful. Perhaps that was because there was only 35 minutes running time on it; perhaps it's because it never saw any real load--the test stand doesn't have a pressure plate or torque converter on it to push the crank forward.
If you still have the block apart, I don't know why you couldn't verify the straightness of the cap with a square or straight edge firmly placed against the main web of the block, and then using a feeler gauge. Similar to checking for head warpage with a straight edge and feelers.
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