Wow - great follow-up post! I wish my STS had a little more juice. From your description of the restriction in a stock exhaust I can see why the Corsa catback system can make such a difference.
I agree that adding another injector would not do any good. I doubt your going lean and that intake is not a wet design - you would most likely not be able to deliver a fine enough mist of fuel nor would it be evenly distributed between the cylinders. If you really are lean you might try somehow raising the fuel pressure a bit but I don't know how easy that would be to accomplish nor do I think it would really help.
If I had to guess, I say one of two things - either you're getting some spark retard due to false knock during the upshift (the knock sensors may be reacting to some noise generated by the new exhaust configuration) or the torque curve of the motor has shifted and there is a drop in torque in the low to mid RPM range. This is often the case when significantly lowering exhaust restriction, and it could be most noticeable in the higher gear just after the shift before the RPM's come up.
Chrysler Corportaion has built some good cars and some good motors - no doubt about it.