The only thing that will let you tune your PCM through software is Superchip's Custom Tuning Pro Racer Package or SCT PRP for short. It's not cheap at $800, but it lets you change
EVERYTHING.
A cheaper alternative is just the Xcal2, but it only allows basic modifications AFIAK.
Modular Depot and
Brenspeed carry the SCT PRP.
I've heard that Modular Depot has crappy customer service, but their forums are well worth the troubles. But Brenspeed has very good prices. Warmonger (I think) got an xcal2 and the PRP software for $670.
Thread in the FI forum talking about the SCT PRP.HTH,
BP