I've managed to find a replacement rear gearbox case in which the bolts do line up. I'm going to dismantle the old box and rebuild it with the new rear case. I just hope the changes turns out as smooth and slick as the old box because it's a beauty! The rear casing that's on must have been a dodgey one unless it's come off a different bike, an A7, B31 or B33 perhaps? I haven't had it off to check the part number yet. I was under the impression all of the pre unit gearboxes were the same, just the sprocket sizes were different.
Yes you're right, there was something wrong with the alignment because there was ware on the side of the old gearbox sprocket suggesting there had been some twisting going on.
Thanks for the info about the re-bore, I've ordered some +60 pistons and taking the barrels to a place my dad knows for re-bore once they have arrived.