did the daytime trains a few weeks ago: in Munich, take the Austrian train to Villach. There, hop on the train to Zagreb. Very nice scenery.
Munchen Hbf: 08:18 EC111 to Villach arrive 12:43. Restaurant on this train.
Villach Hbf: 12:53 arrive Zagreb 17:13. No food/drinks on this train. Bring your own!

For the night train, I couldn't get tickets on Bahn.de (also not via the raildude link). So it's best to give Deutche Bahn a call. When you buy a ticket, it's always for one person, so in order to book both beds in a compartment, you have to book both tickets together.
http://www.bahn.de/i/view/USA/en/abo...-offices.shtml