After copying the directories across, you will just need to set the permissions so have a look at this thread:
Mass setting NTFS permissions
Or you could do something like this (not production level but should work):
You will need to run this on the server and make the changes to match your network. It will bring up a quite a few Dos windows, dont worry its supposed to do that so just let it carry on till its finished and it should work quite happily.
Dim oFS, oFolder, WshShell, strPath
Set WshShell = WScript.CreateObject("WScript.Shell")
Set oFS = WScript.CreateObject("Scripting.FileSystemObject")
'change local path
strPath = "d:\users"
Set oFolder = oFS.GetFolder(strPath)
for each F in oF.subfolders
WshShell.run "xcacls " & strPath & "\" & F.name & " /T /C /P " & chr(34) & "Domain\Domain Admins" & chr(34) & ":F /y",,True
WshShell.run "cacls " & strPath & "\" & F.name & " /T /C /E /G system:F",,True
WshShell.run "cacls " & strPath & "\" & F.name & " /T /C /E /G administrators:F",,True
WshShell.run "cacls " & strPath & "\" & F.name & " /T /C /E /G Domain\" & f.name & ":C",,True
set oFolder = nothing
set oFS = nothing
set wshshell = nothing
I am assuming that you dont have a clash in usernames and the home folders are named according to the username.