So as it turns out I'm an idiot and made a super stupid mistake, Thankfully it didn't hurt anything at all and I've since rectified the error. I know everybody wants to know what I did so I'll tell you all. There I was, going along, minding my own business working on modifying the theme and the css on the website to make the header graphic a little larger so you could more easily see what is going on in the logo and I kept messing things up. I had the CSS in three files, a main css, 960 css and my override css file. The main css controls most of the style the 960 file controls the styling on widths when the site is displaying at a width of 960, the override file just has some random bits of css to override small bits that don't follow standards. I had two things I was trying to adjust, the width of the main header graphic, and the location of the search bar. No matter what I did nothing seemed to work, the areas kept pulling in information from the wrong files. I was doing an inspection on my CSS with Chrome and saw my values but they showed as being invalid. I took a little closer look and realized that I was missing the trailing px behind the the values. The css was right all along but the browsers didn't know how to interpret the numbers. I added my missing px's and now everything is working, as you'll notice if you look right above the header graphic is wider and the search bar follows closely after.
    I still have to do some color stuff, like changing the header background color so you can actually see the logo. However I've accidentally messed up some other settings so I can't change the colors on the website, I'll either have to fix it or do it all via CSS manually, which honestly wouldn't would be that much harder, but I'd like the fix the broken things so they don't cause other problems down the road.