I was in your same shoes after I upgraded to some 295/70/18's on my stock Altitude wheels. After doing a lot of research I ended up buying the Superchips FlashCal. One cool thing about it if you decide that you need a little more performance out of your JK is that you can install the Paq part for $150 when you register and update your FlashCal. I think about it here and there to see if it would be worth buying the performer software to compensate but not changing my 3.73 gearing. Also having the LCD and it being a backlight screen is really nice where your thumbing through the simple menus on what you'd like to change.
2012 JKU Altitude: TF 2.5" coil lift, TF brake lines, TF quick discos, TF tire carrier, Bilstein 5100s, Spidertrax 1.5", AEM Dry Flow filter, Bi-Xeon HID kit, Superchips Flashcal and 295/70/18 Nitto Terra's.