There should be a Backup utility under System Tools, but if there's not, any good 
third party backup software will work.
Use a USB drive or a spare internal hard drive and run a backup of the present O.S. 
during a time the server is not needed. Save it to one of the drives mentioned above.
When it comes time to start from scratch (hopefully soon after the backup was done), 
wipe the server out and do a fresh install. After Win2003 is done installing, use 
the backup.
It should set the server up as before without you having to it manually.

Good luck!

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