Like John says, you either build knowing you need to set a certain distance or you dont. I do on all my engines. As a result, a typical rebuild gets align honed(the other machining operations use the cam and crank bores as indeces to set up the machine), then bored and square decked to square everything up. There's a HUGE difference in quality between a typical horizontal miller and a CNC type block machining center. And a price difference in the work. Avoiding issues like this is why some pay more. Then theres the rod lengths (and differences between stock and aftermarket replacement and good aftermarket replacement), and crank stroke length and indexing. WHen all that is accounted for in the machining, you can set a real distance. Otherwise you're just making a half-behind effort and living with the result. AS Bill said, now that things are at this point, it could get expensive to fix. But it throws off everything if the deck is angled. Cylinder pressures, pushrod length, intake fitment, quench distance, cam lift, not to mention gasket integrity and sealing capacity. There's three ways to get machining done: Right; functional; and not functional. Sounds like you got functional which is probably fine for your use at this point. Teh fix would be to take the stripped bare block (cam bearings have to come out for the fixture) to a shop that can square deck (decking as I said, is NOT the same as square decking, and old school millers do not have teh capability to do it) and have them correct it for you. Then reassemble and the differences will only be from rods and crank issues and only effect the cylinder pressures.