HP Tuners software for the stock PCM or the Holley hp/Dominator setups are probably the best place to start. There's some decent time learning right there--I might get to it myself in a few years, as I just stuck a Gen IV LS in my Falcon. Tons of power seems to come just from cam swaps and tuning in these motors, so there's a lot of homework to do right there.
I'll be keeping the VVT and cylinder deactivation stuff on mine (along with the DBW throttle), because I'm all about efficiency . . .
I'll look forward to any info dumps that happen here.
