Running FAT32 partition on Win2003? Well I would convert it to NTFS for sure, that way you have more control over your folders and files.
We don't install unnecessary software on a server machine in the first place, so when you do and you need to uninstall it, which usually means having to bring the server down for a restart. Time=Money, every minute your server is down it cost the company money, plus do you know how long it can take for Win2003 server to start up into the desktop again? Could be up to 20 minutes, I've seen it take that long, so the point is, don't install unnecessary software in the first place, or wait to remove it after no one is using it. Installing unnecessary software and services creates more complication and adds more to the security problem. Keep the server simple.
Users account should be limited, only permit what they need and deny the rest. Its a simple concept I follow all the time.
Windows file sharing and NetBIOS is ok in a small network, you have NTFS security and Active Directory. Try FTP?
Taken extra precaution when opening files on Win2003? I dont know what you are using it for but you have the wrong idea about Win2003 server, its not a workstation. You dont use it to browse the Internet; actually you dont even use it like Windows XP. You configured what you need and you leave it alone with a password protected screen saver.
That's enough to keep you busy for awhile.