Is the tranny crossmember bent in any way? Another thing to check is how close your engine sits to the engine crossmember. (Does the fan come real close to hitting the bottom of the shroud?) Sometimes (especially on cars that have been drove hard or have a lot of miles) the engine crossmember tends to "spread out" ever so slightly, letting the engine sag and throwing off the pinion angles. Just something else to check.
Still comes back to the basic pinion angle deal.