Yeah sorry I couldn't help more, i'm only just getting my head around javascript myself. It's a great asset to know if you're doing allot of web administration.
I followed this tutorial for on hover popups
www.calcaria.net/javascript/2006/09/java...over-
html-popup.html
I can recomend the open source shoping cart component Virtumart. You can turn off the payment processing part of it and use as a catalog system. It allows for downloadable goods so it'd be perfect to managed all your pdf's. You can then make every one login into your joomla site before downloading. It's used allot and is constantly being updated