I misunderstood what you were saying about the pump. I was talking about installing the complete pump and you are talking about bolting the halves together, my mistake.
Are you saying the manufacturing tolerances on the pump halves bolt holes are loose enough so that when all the pump halves are lined up enough to install all bolts and everything is torqued to spec, the pump halves can still be seriously misaligned? That seems.....like a serious design flaw.
I have a bushing driver set and I am learning how to use them properly like anyone starting out. Part of that learning process is making mistakes, observing the results, and correcting the method (driver alignment, amount of driving force, etc). Did you pick up a bushing driver set on your first day and start perfectly installing bushing or did you mess a few up and learn from that?