Wonder if the machined interface where the trans mounts to the engine was done at an angle and the mainshaft is not square to the primary. When they went to the trans engine connection the fit became critical.
Went back and reread what they have done already and since they changed the trans case if the problem is misalignment it would most likly be the engine interface not the trans case. Checked one of my catalogs of seals and for the most part .003 missalignment will cause seals to leak. I'm sure they have already checked the mainshaft for runout.
Joe I wonder if the seal springs have grooved the shafts ?
Not sure they checked that but I'll ask them tomorrow. Once they get the primary off I'll ask them to put a straight edge across the motor and tranny and see if there is any alignment issues. Thanks Don.
Not sure you will pick it up with a stright edge. It would be the stacked dimension from centerline engine crank to centerline trans mainshaft. That dimension would have to be within .0015 of the inner primary centerline at crankshaft opening to the centerline of the mainshaft bearing. They can check the mainshaft runout with a dial indicator.