Roush Supercharger and Auto Trans

Call Joe at Chicane on Tue. I remember him tuning a 99-02? auto vert with a Saleen blower on it. It had some issues but he worked them out. If I remember, it had a similar problem. I can't remember if he swapped torque converter or not but it was about getting the rpm stall correct.

www.chicanesport.com

Isn't the Aode what was used in earlier mustangs?
I believe my explorer has an Aode in it, and i was having the same exact problem as you, i'd hit the limiter and it would cause a sort of up to down to upshift.
BTW, the truck has a 5.0 with a supercharger on it. (just so you understand why it was hitting the limiter).

I put a baumann engineering shift kit in it, and problem was solved.

http://www.becontrols.com/products/aodecat.htm

If it fits your vehicle, it's awesome, you can do torque settings from levels 1 to 3 to compensate for the power of each individual car, and you can choose from firmness levels 1 to 5, i used 3 because i'm a wuss and you can always go firmer but never softer.
If done again, i'd do level 4 (and i will one of these days.

You will either need to have your shifting points changed via the ecu/tcu or a shift kit and throttle body upgrade will work as well. I had the same problem with my 350Z with the ATI procharger. My car would hit the rev limiter and then almost stall...