The car does have the stock 1996 PCM in it, but from what I understand, it's an oddball PCM that was ONLY used in the 1995-1996 3.8 Fbody and it was GM's first OBDII PCM. I know HPTuners doesn't support this PCM, and some scan tools have trouble talking to it. Most 1996 V6 F-Body owners will swap to a 1997 PCM since it is a direct plug in swap. Luckily, GM made it pin for pin compatible.
I have compared PCM pin schematic from a 1997 GTP and my 1996 Firebird and all the pin positions are the same. I could definitely plug in a 1997 L67 PCM and it would run the car, provide I turned off the auto trans related items.
Minor differences-
-The clutch switch in the manual trans config connects to the same pin on the PCM that the neutral/park switch does in the auto trans config. Should work the same, the description says it prevent idle flare when removing load from engine (shifting to neutral/park, pushing in clutch).
-The extra 2 oxygen sensors specific to the F-body connect to pins that aren't used in the L67 configuration. I just have to make sure that oxygen sensors that the L67 computer is actively reading are placed in the exhaust at the right points.
If I could somehow make a hybrid of the the 1997 Fbody manual trans .bin and the 1997 L67 .bin that would seem to be ideal, but I haven't been able to find a 1997 3.8 M5 bin anywhere.
Using the L67 PCM seems odd at first, but it looks to be pretty straight forward just to take the L67 bin and change it so it doesn't worry about the auto trans. After that it's all electrically compatible, pin for pin on the PCM/wiring harness.