I'd strongly recommend you get out and test drive a few to see how they feel to you.
The Zetec with auto is slighly boring yes, but it gets you around perfectly fine and has better gas mileage than the V6 (which may be a concern for you being a high-schooler and prices nowadays). Definitely prefer it with a five-speed if you want. My Contour was the V6 with ATX and it's no slouch though you could feel the transmission taking away some of the power with inappropriate shift times and such.
The auto's biggest detriment is its lack of reliability in this car. It wasn't a well designed model and many have had to be rebuilt/replaced between 70K and 100K miles. Additionally, if you enjoy driving at all it is fairly sleep inducing.
However, you're not going to find a Zetec with the options you're looking for (power locks and windows, leather, fold-down rear seats, tachometer was not *commonly* available on 98+ Zetecs with MTX since they were the cheapest line Contour available, and I don't think keyless entry came on any of them). To get fold-down rear seats on a 98+ you need to get an SE Sport (highest Contour model aside from an SVT) with cloth or leather -- any other trim with cloth seats won't have them. You can tell by the cloth pattern, if it's a zig-zag style like
this then it won't have them.
Quite honestly with the features you're looking in a car, you're looking to buy a loaded 98+ SE Sport (pretty rare, especially to find one with MTX; and next to impossible to find a loaded 98+ Mystique with MTX) or an SVT. You may want to broaden your search to include SVTs; there are several in the $4K range nowadays.
As for driving stick, I personally forced myself to learn by buying a car with one and having Dad teach me. Nobody I knew at the time had a car with a five-speed except for my college roommate, and I don't think he would have been willing to potentially ruin the clutch with me learning on his $20K car
