I noticed you have a two door. Here's some good ole advice from first hand experience.
If you go with the 3.5" kit on your two door you will absolutely want to go with the X-Factor. You will need the upper control arms front and rear to get your pinion angle (drive shaft angle) corrected and your steering lined out up front.
I run the 2.5" Max Travel on my two door with 37s. I have added the rear upper control arms to mine to push the axle back a bit and gain more clearance around the tire in the back wheel well.
The 2.5" Max Travel and 35s looks perfect on the two door with full or cut flares. 3.5 and 35s is going to leave you quite a bit of room in the fender wells and cause you to spend more money than necessary to run 35s. I am referring to the need for driveshafts, upper control arms, ect.
Here are some pictures of my JK with the setup I mentioned:
This is the most recent with a flare posing on the front:
This is without any flares. The orange Jeep has the 2.5" Stock Mod with 35/12.50R17 BFG KM2s:
Here's another view:
Here it is all flexed out on a forklift. LOL
My buddy Will has the 2.5" Max Travel on his 2 door as well and runs it with 35" Toyos. (nc_fjizzle)
In regard to gears, if you've got a six speed 4.88s will do you good for 35s. If you're wanting 37s eventually just go to 5.13s if you do it now. You'll be surprised by how much power you actually have with a 6 speed and larger tires though. It's NOTHING like the automatic which goes into Stevie Wonder mode and constantly searches for the right gear.
If you have any detailed questions post them up or shoot me a PM/email. I'm happy to help and only want to make sure you don't blow a bunch of money that you don't need to.