What are your plans for the JK? Is it just a DD or a Offroad machine, flattop fenders will gain you a few inches along with the puck you might be good for a DD. Depending on a lift and how high you go you can run into alot of money.
Your Rubicon should have 4.10 gears and with 35's you should be ok for a DD. You'll also need to recalibrate your speedometer.