Unless you are a certified tuner or know 100% what the heck you are dong, I wouldn't mess with those tune options.
The only tune options I would even consider are gear ratio, tire size type calibrations.
The tune you get from MPT will take in account what you have and believe me you will notice a difference with the MPT tune. Be patience and wait for it. It'll be worth it. You really wouldn't have to adjust anything after they send you the tune until you get future mods that require an adjustment.
Cobb Access Port
MAPerformance Tune, CAI, and Intercooler
NGK 6510 Sparkplugs
Everything else is for show.