That's a fairly easy swap, I replaced my '97 TJ's AX-15 with the 32RH automatic 16 or 17 years ago.
You'll need a replacement ECM (engine computer) programmed for the 32RH transmission, different transmission mount, a minor modification to the skidplate to accommodate the different position of the transmission mount, a flex plate to replace the flywheel, shifter (OE console is ok), and odds and ends like mounting hardware. The mounting hardware like the required low-profile bolts for the torque converter might be time consuming but with the Mopar parts guide (which I have a copy for) it shouldn't be hard to locate everything.
You'll also need to replace the output shaft seal on the 32RH with an extended version which is an easy thing to do, you don't need to open the transmission to do it. Its output shaft seal needs to be made longer so the input shaft from the transfer case will be able to seal that opening. Your 231 transfer case has a shorter input shaft which is what the AX-15 transmission needs. It's too short to seal the output of the transmission so ATF will pour out unless you replace the seal with an extended version which is available from several sources.
On the brake pedal conversion that's a non-issue. You can leave the original brake and clutch pedal installed which actually works great. I welded a connector bar between them which makes it really easy to use your left foot on the brake and right foot on the gas while doing technical trail stuff like rock crawling. Or not, you can remove the clutch pedal and just use the slightly smaller manual-transmission style brake pedal which works just as well.
Here's a photo of that setup on my previous TJ...
I got mine installed in, I think, one weekend. Once the 32RH is installed and working you'll be smiling from there on.
I can answer, probably, most of your questions as you go along if you decide to do this. The 32RH is a GREAT transmission, it was one of the two best upgrades I have ever done. The other being f/r lockers.