Align bore is enlarging all the bearing saddles to correct for case warpage, bearings are available in sizes to deal with this, just make sure all the saddles are cut the same amount, depends who did it, Iv'e seen VW Canada rebuilds that didn't touch #4. You would need two different sets of bearings to deal with that.
As for the thrust you need bearings with an o/s thrust as well, same seal as stock.