You don't need to re-gear based on lift. Gearing is affected (*)MOSTLY(*) by tire size changes. Yes, being up higher, or adding a lot of weight, DO have an effect, but it's not nearly as large.
As for getting through rocky trails, tire size is where you gain ground clearance for the lowest points- the diff covers. If you want to avoid smacking them, a good set of aftermarket diff covers (River Raider gets the nod from me), and a set of taller tires are in order. To fit larger tires, you'll need a suspension lift- not a lift to clear rocks- to fit tires!
As far as all that goes, do some reading- figure out what others are running to clear a certain size tire- a general rule is ~1" of lift to clear a 33" tire, 2.5-3.5" of lift for 35's, and 4-6" of lift to clear 37" tires. Having a lot of lift over not a lot of tire (ex. 2.5" of lift over your 32" tires) will look doofy, especially on a DD. It will also likely reduce fuel economy. It will, however, allow more ultimate flex in big rocks if you disconnect your sway bars. But, again, not going to reduce rock hits on your diff one little bit.
Not sure what gears you have, but the OEM 3.21 gears (standard with the 6-speed) are SHITE. They're not even good enough for the OEM 29's on the base model, let alone 32's. If you have the optional 3.73's (with 6-speed, standard on auto), those will be OK for up to 33's, but not optimal. Rubicon 4.10's are decent for 33's, and shite for 35's. Yes, I know people will tell you they run 37's on the 3.21's or some other crap, but I garuantee their rig is shiny underneath, and can't crawl over a pebble. Gearing is what makes a 4-wheeler. And tires, of course.
Don't be afraid of re-gearing. It's relatively painless, if expensive. And I'm not sure why you're anxious about extended brake lines. They're necessary past 3-3.5" lifts, not too spendy (maybe $100 per axle), and EASY to install (give or take 1/2 hour of bleeding the system).
As I said, though- do a bit of reading, figure out what you need. In the meantime, wheel it stock, go SLOW, and enjoy! Upgrades by attrition and need