After quite a few hours spent studying, a few e-mails to IHMC tech support, a couple of conversations with Jack and an e-mail from Brian D-G I was able to successfully install the new CmapServer on the designated virtual machine at the district! Finally!
3 down, 1 to go! Then, I'll be able to take the old server off line, talk to Go Daddy! to change the IP's of mpsscience.org to the new server, then start them and... no one will know the difference except the site will become quite a bit faster... Slowly but surely!