Thoughts on going to 35"s

4.88 is appropriate for the 2.5L four-banger and 5-speed for 33's. For the 4.0L engine and 5-speed and 33" tires, you want 4.56. :)
 
So I would do 4.56 gears for 33" tires or 4.88" for 35" tires. I recommend Revolution gears for this.

You'll need an SYE (I suggest the Advanced Adapters SYE which will also come with a new double cardan driveshaft, which you'll need as well).

In addition to that, you'll also need to beef up your front and rear axles with chromoly / alloy shafts. I think everyone on here is going to suggest Revolution (and I highly suggest them as well), so talk to @Garza for a deal on those parts.

In addition to that, you'll need a new cable shifter for your transfer case, another thing that @Garza can set you up with for a good deal.

If you already have a 3.5 lift, I would add a 1.25" JKS body lift which will put you at 4.75" which should be just enough to run 35" tires, or easily run 33" tires.

The fenders will be another issue. With stock fenders and fender flares you should be fine as long as you set the bump stop properly.

However, if you want even more flex room, you could get something like the Metalcloak fenders, or a more affordable option like the Smittybilt XRC fenders or similar.