The JKs have huge wheel wells. You can run 35s with no lift,but even with hacked stock fenders or aftermarket it'll rub on anything more than a speedbump.
A 2.5" lift will easily clear 35s,but you'll likely still rub occasionally. I put a 2.5" Teraflex coil lift on my 2010. The lift,LCAs and a JKS track bar took an afternoon to install.
Personally I wouldn't run 35s on a stock Rubicon if you plan on wheeling it. The front D44 aint all that,and lots of guys bend or break the axle tubes,if they don't re-enforce the stock D44.
You'll absolutely need to regear it if you go 35s.