There are a few things that I'm looking for in a theme (shell?). Maybe some add-ons will provide these features too. If you can lead me to things that'll work, I'd appreciate it.

Thanks.

1- good program managing
I want to be able to run lots of programs, such as multiple browser instances, etc, and be able to know what all of them are at a glance. I'd like a space where I can see the tasks I have running and enough associated text so I know what they are.

2- auto-hide GUI elements
I don't want to see crap floating all over the place or taking up valuable screen-space

3- transparent windows
I'd like windows that have transparent or translucent backgrounds withough having the icons, text, or borders transparent. I like being able to see my deskop background.

1 - then you're on the right site

2 - see above ;)

3 - don't know, maybe (there's a script in the code section which does that, i think)

Yes, but what do I need to do to achieve that (1&2 at least)? Which build should I use and which themes or add-ons work well?

oh well, use omar's installer, update the build (can be made by a small app included) and download some themes that match your demands, or wait for other to recommend some (i can't really recommend any as i only use my own themes).
however, most probably you'll find that most of the themes will not fully suffice and you'll have to make your own :) ... if so, take some time to have a look into the sticky threads in the general forum, you'll need that.