As you start to disassemble, pull the 1st axle out with the 2nd axle still in and see if it still stiff. The problems started when you put the 2nd axle in; something may be bent on that side only, and doing this will ID the side as bent or not. I am imagining the 2nd axle torquing the side bearings hard in the 3rd member.
Is there any chance that multiple gaskets were installed between the 3rd member and case? I am trying to think of how the gear carrier depth fit into the housing could be wrong.