I've redone the entire brakeline system on 2 MJs now. One with off-the-shelf straight lines with fittings already attached, and once with bulk line and a flare tool (didn't have a choice, as I was integrating in a '95 XJ booster and those fittings are different than a '90 MJ).
For a beginner, I'd recommend the pre-flared straight pieces. Flaring bulk line can be a real pain in the butt. :fs1: I'd also recommend taking the opportunity to remove the rear prop valve from the system, plug the proper port up front, and run a single line to the rear. Also, now's a good time to replace the rear flexy line (I suggest the longer 95 Dakota line) and maybe the front flexy lines too (I suggest the longer YJ lines). Inspect everything associated with the brake system and take stock of what's needed and what should be replaced simply because it's 20 years old and now's a great chance to do it. If too much of your rear brakes are toasted/rusty/bad, I'd suggest looking into alternatives rather than a ton of money on a Dana 35 (I'm assuming that's what's back there).