I was able to find a NOS GM gasket for the front engine mounting plate so I pulled it back off, cleaned everything up and checked it with the gasket dry.
Same results. Even with no gaskets under the camshaft thrust plate, there was still a gap between the straight edge and the shoulder on the crankshaft with the straight edge flat on the thrust plate.
So I made two shims from a pop can. Now the shoulder is flush with the cam thrust plate with no gaskets under the thrust plate. I'm not sure if this was necessary but at least now everything should line up and I can put the crank gear back on.