Ok, so I got the site modules back to kinda where they were before. The javascript drop down effect seems to be working fine on the main page, it's just when you get into the archives that it seems to break down, same is true for the lightbox app. I know it has something to do with the file pathways, otherwise the scripts would be working fine. Really liking this new template style I have up, I will probably tweak it later on, maybe mess with some of the images.
UPDATE: Ok, ok, yeah I know the site is starting to look a bit cluttered, right now I am just playing around with some different MT plug-ins. When I get home I am gonna try and see if I can find a way to compact everything a little better, maybe attaching the drop down javascript effect to the arrow image in each module header, I don't know, right now it's just a thought.