While I don't usually upvote questions, yours was particularly interesting and well-formed.
I don't know what you're using in terms of ordering the JavaScript list, but I have seen Docking Boxes work quite well.

In terms of the Perl part, I could probably write something, but it would be rather redundant and probably not what you are looking for. Like aaron_baugher said, we could help you more if you posted your code, or at least important parts of it.