The easy answer here is to purchase a tool. A set of command line tools (including "audit," which does what you want) are available from Pedestal Software. I have not used these tools, so can not vouch for how well they will work in your circumstances.
The long answer to your questions is that you may need to do a little more than use a batch file -- you may need to develop your own utility. The following Microsoft documents discuss programmatically setting SACLs (audit settings) for files and folders. For Windows NT, Auditing, or the other side of security provides C++ code examples.
Some documentation on the "SetFileSecurity" method (works in Windows NT and above) is available here.
Should you be thinking of moving to Windows 2000, see ADSI article Setting access rights on an object. If you're looking to move to XP or Windows Server 2003, look for information on the IADsSecurityUtility interface for XP.