OK so this is a pretty broad question I just want to see what pieces of advice I can get: so I have been away for college and haven’t had my jeep with me since July, the jeep runs pretty well and doesn’t have many major issues to note. Anyway so I am looking at making my jeep Freeway ready so I can drive it from Washington state to Arizona where I go to college here in May. I am just wondering what kind of things should I expect to have to fix when I get home after college. Right now it is sitting at a 6 inch lift with 35 inch tires and honestly the engine feels gutless turning those tires and doesn’t quite get above 60 mph on a good day.  I understand this may be hard to answer questions for if you don’t know the vehicle, so feel free to ask any questions in the comments. Any advice is appreciated.

Is it on stock gearing?

yes it is on original gearing, 3.55, that is the first thing I’m doing is regearing it. Any suggestion for moderate off-road use and freeway travel. Obviously debating between 4.56 and 4.88

Have you looked at 410 gears ? I think the rpm range would be better , it wouldn't run the engine so hard at freeway speeds .

You want 4.56 gears with 35s, it will be downshifting all the time on the highway with 4.10s. Even with 4.56 gears mine downshifts quite a bit, but when you go to 4.88 or lower the pinion gear on the Dana 30 gets much smaller and is more prone to failure.

Any other things I can do other than gears

If you have an AW4 trans, you'll want to go with 4.88 gears to get the rpm's back to stock with those tires. I run 5.13 gears with my 5 speed Rubicon on 35s. I can drive it 85-90 mph easy.

Both statements are wrong.

Both statements are correct.

Get a set of freeway tires for the trip if you're re-gearing after the drive. And a small utility trailer to bring the big tires with you. I'm a huge fan of Harbor Freights utility trailer.
If you have to drive the beast with those tires, lift, and gears that far, make sure all of the common stuff is looked over like suspension and steering nuts and bolts are tight and fittings are recently lubed. Headlights are aimed correctly....
Personally I would just be worried about all that highway traveling with the suspension lift and large tires being a huge factor. And with your current gear ratio, it could really do a number to the trans and engine with the load. But if you drove it on the road a bunch before and its well taken care of for the most part. There shouldn't be much to worry about.

Yea, I don't think it will be much fun to drive on the highway long distance as it is set up now.

Depending how it was stored among the usual maintenance tasks make sure you can get the wheels off. If wheels have rusted to the rotors/drums it could make an emergency tire change on the side of the road impossible. Put a light coating of anti-seize on the mating surface. As mentioned above a trailer might be a good investment. With that much lift I would avoid putting any weight up on the roof for an extended trip.

If you drive it around with the stock gears and 35s put the shifter in 3rd instead of overdrive.

Would it be cheaper to trailer the truck back to school? Get a friend with a pickup and rent a trailer, then you won't have to worry about prepping the truck for the trip, unless you plan on making the trip numerous times a year.