It could have been that way from the beginning, or possibly the block was line bored and moved the crankshaft position moved. I have seen taper bored cylinders so that they are perfect after 100,000 miles of wear and the ridge at the top removed, preventing a bore job after the fact, decks of blocks off by a tenth of an inch from front to rear, bolt holes drilled all the way through to water and oil passages. Things happen one does not expect in a repeated machining process, but it happens. It could also, in your case, be the transmission case itself, the pilot holes could be slightly off instead of the block itself being off. Remember, in a case like this, if you think about the center of a wheel with spokes that go straight out from the center, a small center position off increases as you go outward, so something that is .010 off center in the middle, ten inches outward requires .035inches correction, as an example. We don't expect these kinds of errors, and usually don't think to check them because they were fine before we tore them apart, but they happen on occasion. I'm just glad you got it fixed.