Hm, i thought i had replied to this, btu it must have gotten lost.
Anwyay, what it might be is the dowel pins being a bit too much of an interference fit. Try getting a couple of the LARGE bolts through the holes and in a few threads so then you know it is rotationally aligned, and once the box is properly supported again you can step back and take a good look at the setup without constantly trying to be getting the box on.
Check the dowel pins arnt gettnig stuck, i usually put a drop or two of engine oil on mine to make it easier to slip them into the gearbox bellhousing.
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