So it turns out that I screwed up the LAR by downloading it off of the web and then uploading it again. For some reason this seems to drop all of the uppercase letters thereby messing up any links and images that are referred with an uppercase letter. I tested out the same scenario on my laptop and it appears that there is no such problem, so I'm going to try to get Erin to upgrade winSCP tomorrow to see if I can solve that problem.
Beyond that oops, it's become apparent that we need to architect a better system for storing files on web_dev. Currently there are many folders and files that I'm not sure who to ask about. We decided today to just have the four main site folders with their info in there. Although, I'm not sure if it will be just that simple with all the other folders floating around.
I'm currently working on consolidating and changing over to php on the ISSE site, which is no small task for any of these sites. I'm waiting on Linda Mearns to go through a bunch of possibly old files and then from there hopefully changeover to php. Once I'm done pushing all of the sites over to PHP we should have a nice start to moving towards Drupal.