From Cobb's website:
The Stage 2 was tuned on a car with a full turbo-back system. If you have pieced together a less than optimal combo of parts or those that were not designed to work together you may not get the full benefits of the Stage 2 AccessECU. Boost may not come on as quickly and the peak power may be down from those that have a well designed full turbo-back system. If you have replaced the first section (second cat or downpipe section) and nothing else, then the Stage 2 map is what we would recommend. Again the results will be far less than optimal, but it will control the boost better than the Stage 1. If you have replaced sections 2-4 (third cat, mid-pipe, and muffler section then you are still Stage 1. You managed to get all except the part that makes the most difference. Again, we want to reiterate that Stage 2 will only get the intended results with a well designed complete turbo-back.
Since I have replaced my DP and Cobb says Stage 2 handles the boost better with that mod than Stage 1, I went with that. I realize I won't be getting the full potential of what a full TBE would offer, but I do like the fact that it's *quite*, stealthy and cheap.
Also, after looking at the full datalogs I think I found that the 4900rpm blip in KC values are from a rise in timing at the particular point, so the ignition timing stays the same through the rpm range. So I'm not as worried as before. It looks fine to me.