Pretty much everything is do-able in litestep. I'm pretty sure a theme could be made to emulate the look and feel of explorer. You'll find answers to your questions about the popup and systray in your litestep\modules\docs directory. Other good docs are found at http://o-t-s.sourceforge.net/ and http://www.residualvisuals.com.

Try editing some themes to your liking, like adding more icons to your systray, editing your poppup, and adding other stuff to existing themes. You'll understand how LS works and you could try and make your own theme.