IMO if you don't plan on doing any off-roading which requires full articulation of the suspension I'd go with the tires 1st, otherwise they may rub.
Your mpg's will drop. How much will depend on the weight, width and tread of the tire. A heavy, wide mud terrain tire will give you the poorest economy.
Keep in mind that your speedometer will be off with the larger tires, which will obviously affect your odometer too. Look into a tuner that will allow you adjust your speedometer for larger tire sizes.
Also, a larger tire usually requires a lower P.S.I. Once your new tires are installed I highly recommend doing a chalk test. If you're not sure what this is, you can just google "tire chalk test". There are plenty of videos out there explaining it.
If your wheels are equipped with TPMS sensors you may get a "low tire warning" on your dash. A good tuner like the Superchips Flashpaq will allow you to adjust the TPMS settings.
Gearing! Gearing! Gearing! Take it from me, I learned the hard way. No performance upgrade will give you the results that new gearing will provide. I know the new 3.6 Penastar has more HP & Torque, but the JKs are notoriously underpowered. Especially the autos because of the deep overdrive. You may be able to get away with it with a manual, but the performance will still be sluggish.