Good start, but...
Not bad for trying to create a functional Section 508 site. However there are a few issues:
High contrast for accessibility fails, links on white backgrounds are actually lower contrast on homepage. High-contrast does not remember settings when moving to a new page.
Breadcrumb navigation on subpages gets lost when on webpage background. Blue link text on blue background.
Slideshow for homepage has an unsupported link "o" when using text-based browsers. I have no clue what this is suppose to be linking to.
Not responsive for mobile devices.
Have you done use cases or at least tried to determine what your most access content is to make it easier to access? I'll be honest, there are way too many links in the primary navigation to find what I am looking for.
I would also recommend add more skip to links, to make it more accessible.