Thanks for the replies Andrew & WPyogi, I got my theme from RocketTheme.com I dont think many (if any) of these errors existed before transferring my website to the root folder.
There actually IS a DOCTYPE defined, but just like the head tag, its being placed all the way at the end of the html (line 2180 of the homepage). I have lightly modified some theme files. But as I mentioned I don’t believe any of these issues existed before the transfer of the site.
I have compared my header.php and functions.php files to the originals and there are no differences.