Like I said in your other thread, I don't know much so I should leave the recommendations up to the real pros on here...but I can tell ya about equipment and my personal preference.
New tacos come with 2 transmissions for the 4 cyl & 2 transmissions for the 6 cyl. If you get a 4 banger, you can choose between a 4 speed auto or a 5 speed manual. If you get a 6 cyl, you can choose between a 5 speed auto or a 6 speed manual. I got a 6 with the 6 speed, and I love it. Its a good tight shift patternI'm inclined to think that desert running would be better suited with a manual tranny than an auto for the same benefits it offers on every other type of terrain...but let the experts on the site chime in too before you trust my word.

Here's my line of thinking. With a manual, whatever the situation, you're always free to stick it in whatever gear you need...you don't have to trust the transmission to shift at the right times, because its been my experience that autos RARELY hit the right shift points...in any car and any scenario other than a sunday drive down the freeway at 55 mph. Also, if you're driving an auto & goose the throttle a little too much around a turn, the passing gear could kick in at the wrong time, over rev your engine & cause your tires to break loose when you don't want 'em to.