OK, so I finally took the plunge and ditched the stock intake box in favor of a CAI. I changed nothing else in the turbo plumbing system. Now I have noticeable compressor surge (aka turbo stall) in some instances.
I'm running a 1st gen DSM BOV (not crushed) directly after the turbo and the vacuum line goes to the brake booster. This set-up has been on the car for a while and worked absolutely great. It was also on my van and on my LeBaron for short periods of time and I never had this issue (van was Mitsu turbo, 'Baron was Garrett).
Could it be that this has always been there and the stock airbox was doing too good a job at masking the sound or is there something else I need to look in to? I don't remember this EVER being an issue on the other vehicles this set-up has been on.
I'm going to alter where the vacuum source for the BOV is from the brake booster to the throttle body and see if that doesn't help, but I'd still like to hear some input.