What I do when I want to move/clone my MDT I make a backup of the deployment share folder.
Once I have this I make my new Server. i.e. SAMDT002
On this I install Server 2008 R2 (Fully patched via WSUS).
Anti-virus
MDT2010 Update1
WDS
Windows 7 AIK
Now setup my MDT deployment share, default values for CustomSettings.ini and Bootstrap.ini
Now I have that created, delete all files inside my DeploymentShare$ folder. And replace them with all the files from my backup.
Now that the files are on, I open all .xml files with Notepad++ and then do a search and replace on all open documents. The info I replace is the OLD servername with the new one.
This is now the server moved.
NOTE: If you still have an issue with it wanting the old server, simply add this to your customsettings.ini
DeployRoot=\\SAMDT002\DeploymentShare$
(this goes under [Default])
Note that I used my new servername, replace that with your own.
same needs to be done in the bootstrap.ini
Please +REP if i helped you, also if you need any more help I will help if I can.