I got busy getting my supercharger buttoned up. My wife and I are leaving with the car tomorrow for a long weekend trip. I had a chance to review your tune really quick.
Most of my time spent tuning is with the LS1B controller, but I'm starting to get into the E38. Do you have a wideband oxygen sensor? If so, is that something that you are able to plug into your Flashscan and include in your log? I flipped through some of your idle airflow tables and they look okay, timing seems okay as well for the portion of the log where it is idling with no pedal input. I referenced this thread with regards to idle airflow:
https://forum.efilive.com/showthread...38-idle-tuning
Also, can you log SAE.FUELSYS? This will tell us if it's running in open loop or closed loop, just a double check.
Engines run properly when air, fuel, and spark are set properly. If you have a wideband, log that so we can see how your fueling looks. Commanded AFR is good, but it only tells us the input and not the output.