I was trying to get rid of the content in the header file but keep the file because of the includes and such. In doing so, when I remove this one div (header-right), it causes my footer to go inside my wrapper. I can’t figure out how to make my footer appear below the yellow box shown in the page.
check for matching opening/closing divs – you might have removed more from the header than you had planned.
a broken html structure is hardly a wordpress problem, even if it happened in a wordpress theme.
also, helping with commercial themes through this forum is virtually impossible without the free access to all theme files.