what is the purpose of the align bore to begin with?
The purpose of align boring is to get the main bearing bores perfectly round, and exactly in line with each other. Stovebolts are particularly difficult to bore properly because all the main bores are different diameters and all the holes need to be cut at once, using cutters adjusted to four different diameters on the same shaft. Add the difficulty of maintaining the proper timing gear fit, and it takes an extremely skilled machinist to get the job even close to right. The bore diameter tolerances listed in my shop specifications manual are in the neighborhood of .001"- - - -2/3 of the diameter of an average strand of hair!
The machine shop owes you another block, properly prepared by a different shop!
Jerry