There's alot of different ways and options to clear 35's. The first thing I was say or recommend is looking thru the "Lift Reviews" at the top of this thread that has pics and comments about people lift kits and pros and cons they found while doing them.
One of the best way now a days is the Low COG approach. Get a 3" or 4" lift and some Tube Fenders to help clear the 35's. I've even seen some people go with 2" lifts and get the Hyline fenders to clear them.
Your next concern for 35's would have to be axles and gears, especially if you want to drive to the trail, hit the trails hard and drive home. This depends on the type of wheeling you plan on doing.... ie rock crawling, trail riding, mudding... etc.
I ran a 4" Clayton SA (short arm) kit on my Rubicon and it had some crazy flex for a 4" SA kit and I also ran Poison Spyder Tube Fenders in the front and cleared 35's with ease.