Bearing clearance is the result of the bearing bore, the bearing shells, and the crank surface. Without a mic and measuring you can't tell which might be causing it. this is one of the issues with plastigage and why if you're serious (and it sounds like you are) then buying the right tools can only help. You're beyond the "street engine" power levels and thigns have to be right, not "ok". In any event, you should be able to get the bearing shells to get the clearance you want. But if it was me, the shop should mic the bearing bores and the crank while you watch (pay them for the labor) and then you can see how it should be done.
