It should fit. You might even be able to install a lightbar over the windshield with some lights and make it fit.
Still, I'd measure. Go to the Jeep dealership and measure the JK you want to buy from the pavement to it's highest point. Then, add 4" for your lift. Then, for each extra inch of tire you'll be running, with stock as the base to compare to, add a half-inch of lift.
So, for the sake of this argument, Wikipedia says that a factory JK is 70.9 inches, so lets round up to 71 inches (you should still measure the actual Jeep you're planning on driving off the lot.) Now, we add 4 for the lift and we get 75 inches.
For the sake of this argument let's assume that the stock tires are 30.5 inches in diameter, which I think is actually correct for a JK. You want to run 35's, so we take the extra 4.5 inches in tire height and divide it by 2 to get 2.25.
Now, we tack on the extra 2.25 inches of lift you get from the bigger tires and your grand total comes to 77.25 inches, give or take an inch or two for spring sag and tire pressure.
Then we just divide 77.25 inches by 12 to get 6.4375 feet, or six and a half feet, basically. So after all is said and done, you should still have about a foot and a half to play around with.
If you hate my explanation of it, sorry, I'm one of those people that likes to work out math problems with long sentences
The actual equation is something like this:
Factory height + (Suspension/body lift) + [(New tire diameter - Factory tire diameter) / 2] = (Total projected height in inches / 12) = Total projected height in feet
71 + (4) + [(35 - 30.5) / 2] = (77.25 / 12) = 6.4375
