Re: 8.8 flange differences?
Sounds like either you're missing washers or the threads in the new diff's flange havae rust built up on the threads at a certain spot. My advice is to chase the threads before going any further.
2009 Ranger Sport 4.0L 5 Spd 3.55:1 Bone Stock
2013 Scion FR-S 2.0L/H-4, 6spd, 4.11:1 Fast Enough Stock