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You can train all the way from Berlin to Zagreb, though it might be faster to take a bus after Vienna into Slovenia. I may be out of date though. You will need buses once you are in Croatia - Montenegro.
As for the Greece suggestion, you will likely need a separate trip for this if you intend to go to Central Europe first(or if you have tons of time). Fly in to Athens or one of the islands using a budget carrier like Easjyet, then fly out of another island. Flying is cheap and quick in Europe if you do that. Taking the ferry between the islands is part of the enjoyment of the trip though.
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