There's a lot of stuff that can be done with the pcm! My first thing was to set my spark/fuel/cam's to the Challenger settings the best I could as the Challenger has the highest power output then I modified my tune from there. Granted my adjustments and settings won't apply to your vehicle as I'm FWD but here's a copy of my tune that's been played with by many tuners and myself, it's kind of a hybrid tune. I will warn you, DO NOT copy the transmission settings as they are for my 62TE FWD transmission......
Attachment 129864
I have made many adjustments to this tune and I keep resorting back to it as a baseline for "MY" car. I use either 93octane or E50-E85 fuel with my mods.....
I have more bolt ons than just a CAI....
Also note that I average 22mpg highway on either fuels with my larger than stock fuel injectors and on E50+ at 7000rpm my injectors do not max out anymore using the bigger injectors I have. My stock Flex fuel injectors at 7000rpm were hitting 105% duty cycle on E50+ fuel so I added larger injectors to help compensate the max duty cycle so now at 7000rpm im only hitting around 75% max duty cycle on the injectors.