Actually, I've been looking into doing this myself on my 04 Alero. I borrowed a friend's TECH-II and noticed that the RPO option for 5spd exsists in the ECM already, so theoretically you can just turn that on with the Tech-II (any GM dealer) and you're set as far as computer goes.
Has anyone actually looked to see if the punch outs are there for the pedals in the firewall? One of these days I need to get off my keester and look
Also, if your looking for beefy Automatic parts, I'd recommend picking up the GM book on building the Ecotec from 300 to 1400Hp. They recommend an Automatic for anything over 500HP and have part numbers listed for HD units that will take up to 1000HP. (they aren't cheap tho...lol)