I just did a T56 swap in my Impala and she drives great, but my problem is that the car stalls when it's in neutral at a stop. It's like the car is in gear but doesn't jump forward. If I hold the clutch pedal down it doesn't die but it starts to die like it's trying to get into gear when I start to release the pedal.

The transmission is freshly rebuilt and I'm breaking it in and the clutch is a Street Twin.

 

Sounds like your clutch isn't completely disengaging. Try bleeding the hydraulics.

 

The car is in neutral though not in gear so it's not a clutch problem.

 

Oh, sorry, read your post too fast . Did you get the PCM updated with an M6 program, or are you still running the stock A4 PCM?