They're not super difficult...but there's a lot of work you gotta do that can be really frustrating. First, you're gonna have to get a bender and bend your new brake line to the same shape as the old...if you've never used a bender, this will be a wonderful adventure while trying to get your bends right. Then, once you get it bent and you get the new line bolted in, you're going to have to refill your reservoir and completely bleed your brakes to get all the air out of the lines. When you replace a line, sometimes, you gotta bleed em a ton before you get ALL the air out of the lines and have functioning brakes again.
As far as Jeep specific issues...I can't say...that's just general brake line replacement I'm talking about.