Take a look at the crossmember itself, specifically the two sleeves where it bolts up. There should be a couple tack welds holding those sleeves in place. Grind those welds down (just the welds) and slide the entire crossmember along those two sleeves. Once you have it lined up, retack those sleeves. You dont HAVE to retack them, but that will prevent them from vibrating.
Later years have the same issue when swapping the AOD for a T5, or vice versa. The exhaust hanger at the transmission also differs. The auto is straight while the manual is offset. I can only assume your 79 is the same way, so check that out if you havent already. Post some pics if you have them.