Hi Gary,
Couple of thoughts:
1) Shifting - you do seem to shift *politely* for having Stage I installed. It probably goes against the WOT optimization and causes the lag. (you are taking it easy by its standards.) Oh, and this is why I'm lazy and drive automatic. Mash the gas and go. No human mistakes or delays.
Stage I Manual Product Pitch:
Increased WOT and part throttle boost
Enhanced 1st gear boost schedule for a higher performance launch <- !!!
Optimized calibration for the Mopar Blow-Off Valve Conversion Kit (4510548)
Improved turbo response
Boost hold feature during WOT shifts <- !!!
Soft rev limiter
2) Loudness - Your car is definitely a lot louder in the cabin than mine, however I have the stock exhaust and the turbo is setup for 'turbo lite', a lot less boost. This could explain why it is louder in your car than you'd expect. I'd try comparing it with someone else with a Stage 1.
3) Problems indicated by noises - the lack of any error codes means that it's running fine as far as the computers are concerned, so i doubt the mechanicals are out of order. (You'd expect a misfire warning or some other warning.) All of the flutters and whizzes sounded in line with what my car sounds like.
4) Bath Time for me - Yeah, it's definitely time for a bath. It's a bad sign when your Graphite Metaillic Platinum Series looks like a Black PT with Chrome.

I'll probably knock the salt off on Friday.
- AJ