Got a S9b LSD tranny, with some 96 spec itr shafts (non abs) and some B16a2 shafts, they came out of this box but i am struggling to get the left side back in, it is millimeters off going fully in and wont line up with the bearing bracket on the back of the block.

I have tried both the same shafts in another s9b box and they go straight in no problems, cant see anything out of line in the box either, any ideas?