Here is what I've found out. If you can get a dealership to put in a non flex fuel ecm, and do the trd flash, you will have basically what the non flex fuel guys get. You can buy the super charger and install it, install a unichip, and have it custom tuned. The unichip solution tends to grenade transmissions because the chip only tunes the motor, not the tranny. Or go to Hennessey ... and I bet hennessey puts a non flex ecm in, and does it up.
As far as I know, all of these options would void your warranty. Once I hit 50k Im getting a new ecm (Im a flex fuel also), installing the super charger with an ase cert mechanic (my local dealership SUCKS) and finding a dealership that will do the flash.