I took the old website, turned it into a zip file and posted it to the root of the departmental account.
I then deleted all but the clipart folder in the old site on the department account
I then uploaded the new site to the account and did some quick testing, specifically of the php and included files.
Thanks to Greg for noting a couple of bugs which I fixed.
I also wrote a readme file and posted some technotes to the root of the new site for the use of future maintainers of the site.