I don’t believe that this is much different from moving Notes databases to a new server.
1. Configure your new Windows server.
2. Install Domino on the server.
3. Install domino.doc on the server. Domino.doc adds additional code to the Domino server (additional api calls).
4. Create your new directory (name and address book).
5. Copy your domino.doc databases and templates from the Linux Domino server to the Windows server. I would not copy any other Notes databases. I would not copy any of the regular domino templates over. But to program domino.doc databases, you must use templates. You should not directly modify the actual databases.
6. Test. Most of your problems will be one of two kinds. (1) access control list/rights issues (make sure your directory/nab has the correct domino.doc groups). (2) You will probably have to resign the databases with the new server’s ID.