Hmmm, not sure I fully understand your comment: the sump can only go on one way, with a dozen or so bolts, so are you taking about the gearbox / block mating faces not aligning (ie the lateral axis in line with the crank) or the actual bolt holes (ie perpendicular to the crank)?Did you line up the flywheel end of the block with the flywheel end of the sump? I didn't align mine properly and had to take the sump off again and re-seal so that the gearbox would mate with block and sump.
I guess I will find out next weekend when the gearbox goes back on... I hope it will fit.