The Tonneau cover is the way--if it isn't needed, just man-handle it off (the cover says 2 ppl required, but I don't have that luxury most often, and I still get it done). The bed extender is nice, and if you really don't need it at a certain time, just pop it off and throw it on the folded down back seats
The power window is essential...the power rear window is what
makes the Sport Trac the awesome vehicle that it is. Without it, you just have a topless explorer, which is just lame.
The sunroof is a really nice option--it has so many uses, almost as good as the rear window.
I didn't get a trip computer because they didn't exist in 02 for the ST--all I got was the compass and thermometer...but those are awesome features, and if you can get a trip computer on top of that, you won't be disappointed if you do.
Running boards have their uses as well, but I could see going without them. Since the new ST doesn't come with a bumper hitch, and you can't add a better hitch, I'd say that the class III man hitch is a good option, if not you will never really be able to tow anything worthwhile. (Tis better to have it and not need it, than to need it and not have it)
My lengthy 2 cents.