centering rear end

If it has green bearings the axles should be perfectly centered if their identical axles. What I was talking about earlier only concerns stock type adjustable bearings. Something isn't right there. Have you pulled the axle that's sticking out too far and checked to make sure the bearing is pressed all the way on? If not I'd do so. Another thought is I wonder if someone left the thrust pin in the center section when they installed the green bearings? If they did that's possibly the reason for the problem. When you assemble a rear with green bearings on the axles you usually slap one axle in and tighten it down. The first axle will go all the way in because there's nothing to stop it. Then you install the second axle and if the thrust pin is still in the differential it stops that axle from going all the way in. If you don't find a problem and since it has green bearings you could try swapping axles from side to side and see if that makes any difference.