Remove their admin rights to the machine. And any good app will get its time from the server not the client. To watch when the time is changed enable auditing on the local security policy of use of user rights. Jim
Write a script to clean it up then. But I would not remove those folders. Your asking for problems if you do, and how much space do they take up anyway?
Ok basically it boils down to this. Shutdown current PDC. Promote a BDC to PDC. Ensure replication. Upgrade OS to Windows Server 2003. Ensure functionality. Upgrade the rest of the BDC's to Windows 2003 DC's Sell Old PDC on Ebay.
Also, if you really want to understand what is going on, use VMware to set up a virtual lab so you can configure the servers and actually do the work instead of just reading about it.