Have you looked at icacls? You could just have icacls spit out the acls to a file and then use the file to set permissions on the destination.
Or you could just use xcopy to copy your folders to the new inetpub/wwwroot and then replace the files that need replacing:
Copy a Folder to Another Folder and Retain its Permissions
Click Start, and then click Run.In the Open box, type cmd, and then click OK.Type xcopy sourcedestination /O /X /E /H /K and then press ENTER, where source is the source path for the files to be copied, and destination is the destination path for the files.
