Okay! Just as an epilogue I guess. Went through the motions of installing the latest service packs and all the hot fixes. The longest part is we figured that it was a good idea to reboot the server every time it asked to (which was after every installation).
All in all it was a relatively quick process. Only about an hour and a half (backup of root directory on server included) to get the service pack and hot fixes all installed and tested. So far I haven't had a user come to me with an issue.
If someone is doing a massive upgrade like this one I recommend not starting the blackberry services until the very end and creating a full SQL backup before you start the process so when it asks if you want it to backup the SQL server you can tell it no. Next upgrade is planned to happen with a new server to host 4.1 for Exchange. Thanks for all the help.