Block out of square

I wouldn't use shims at all. The thing that gives the mating surfaces all their strength is the fact that there is so much mating surface (area). If you shim it it will greatly decrease the amount of mating surface. The total stress put on the bell housing surface (which is the weakest surface) will be transferred to the area around the bolts as opposed to the whole mating surface. You can't machine the bell or you'll throw out the trans/drive-line alignment. I'm a machinist and don't see why a machine shop couldn't skim the rear mounting surface of the block. All they would have to do is get the rear face of the block "square" with the crank center line?? The only draw back would be that it "might" put the trans/convertor a little closer to the block??? But that small amount (.040") should be OK because of the torque convertor to pump clearance unless you have a standard trans then you might (doubtful) might have some input shaft interference??
It would be difficult to machine 1/2 moon shim, possible but difficult. If they align honed the engine it's possible that they did it wrong (causing your problem) unlikely but possible. You could easily check for "squareness" if you use a large "good quality" square to set against the bare mains and see is there's a difference between the top and bottom of the rear block surfaces?? Or if you set the back of the block standing on a flat surface (vertically) then set the square against the table to see if the mains are square to the table. Treblig