Sounds like a couple issues. 1. You need to tune out the auto transmission on the pcm and possibly the theft system. 2. You may have to jump two of the wires on the harness that used to go to the shifter on the auto transmission (pcm is looking to see Park or neutral).
2004 Olds Alero 3400 v6 15.32 @ 88.69mph Bone Stock
1999 Olds Alero 2.4 to 3500 swap (running), Ported heads. totaled by a honda
2002 GAGT 3500 swap. parting out
1993 c1500 turbo 3100 swap 5psi.
1976 Cutlass 350 olds stock for now