Wow, thanks for all of that. I will try a fresh install but I have a feeling it will work fine. I'll take a look at the javascript and see if I can figure it out. If you or anyone else out there can debug in the console go for it, I'm still learning a lot of this stuff. The "#" vs real link doesn't seem to make a difference.
Thanks for the tips on the other stuff too. It is all really good advice. Just have to figure out how to implement it.