As I mentioned above, I have a "big front mount" (CAS V2), so I'm sure all that volume is part of the issue. Basically, my combo is about as conducive to spooling (and subsequent flutter) as one could get. TA-49, loose exhaust, big front mount, loose converter, and check-valve boost control. The data I sent to Bob included 70 "idle, open throttle, close throttle" runs. Even if I just opened the throttle "a little bit" (say 1.0 volts TPS) for a short time (say one or two seconds), enough turbo speed would build that I would see long periods of backflow and flutter during the deceleration. That would cause the engine to stall in many cases.
A blow-through MAF or TPro (get rid of the MAF) might be a next step for me. For now, I am fairly sure that the existing "anti-stall" features in the chip can prevent the stalling. The threshold for "anti-stall" activation just needs to be lowered significantly for my car.
Once Bob and I get our email straightened out and I get some information from him, I will continue working on this. I am hoping that I can get this done this weekend, since I'll actually have time to work on it.