I have wheeled both a 99 auto Trooper and a 93 manual Trooper quite a bit. I wheeled the 99 mostly in Moab, the 93 I have wheeled in Moab and here in Minnesota.
The autos are easier for a novice to wheel, compared to manual. Rock crawling with an auto just calls for a steady foot on the throttle and let the torque converter do the crawling. But, as noted, going downhill or off ledges calls for a very careful foot on the brakes lest things get out of hand. If you get too much momentum you are on a sleigh ride to the bottom, often accompanied by one or more loud noises.
Now, when I said the autos were easier to wheel than manuals, there is a way to level the playing field. If you install the 3.07:1 Revolution (formerly Teralow) low range gears in a manual, it makes all the difference. With stock gears slow speed rock crawling is often a series of lurching and crashing over the rocks, whereas with the crawler gears you have the ability to go slow enough to pick your lines as you crawl, and generally make a much more controlled (if less dramatic and exciting) progression through the obstacle.
And on downhills with a manual you can generally use engine compression to coast down ledges and hills without ever touching the brakes, a much less risk of things getting away from you.
And last but not least, the MUA5 manual is a much more durable beast than the 4L30E auto.
Hope this helps, let me know if you have any more questions.
