More than 3" and you need the SYE, and a new rear driveshaft, that's about a grand for those 2 parts.
You should be able to get a decent quality 3" lift for around $500-$600, and it will have everything you need. (Stick to the ones with the full rear spring packs.)
You and a couple of bodies should be able to install the kit on a Saturday, if you're at all mechanically inclined.
I ran a 3" Skyjacker kit and 31's on stock rims (with very minor fender trimming) for a few years, and I really liked the setup for all around daily driver and trail duties. I even used it to pull a trailer across Canada when I moved out west where I am now. I didn't re-gear and it seems to have no trouble on te highway or the trail.
(Mine is an auto, and they have 3.55's from factory, the manuals come with 3.07's apparently.)
I really liked that setup, but I wanted to go bigger and I now have a 4.5" lift from Rubicon Express.
RE is pretty good and has a very good reputation, but it's not perfect.
The Skyjacker kit I had was ok, cheap when i bought it, but after my first weekend of 'wheeling I had to get an additional leaf added in the rear because they had sagged so much. That was a disappointment...
Unless you get into serious offroad stuff, the 31's are going to take you through a lot of trails with little to no problem, and you maintain a really high level of the original ride quality, just a bit stiffer with the new suspension.

And if you do start getting into more serious offroad situations, you're going to want a locker, or two, bigger tires etc. etc. At that point it would be smart to switch out axles and gears before you have to buy the new rear driveshaft.
If I was to do it all over again, I would have stayed at 3" and the 31's and spent my money on bumpers, a winch, spare carrier on the rear, front ARB locker and some other goodies.
My XJ with 4.5" lift on 33x12.5R15's is not the ideal daily driver...