Croatia

We're also flying into Zagreb in September but plan to take Croatia Airlines between Zagreb and Split to save time. We're picking up a rental car in Split to drive up the coast - another possibility for you. You could fly to Dubrovnik on Croatia Airlines, ferry to Split, rent and car to make your way back to Zagreb. It's not very expensive to fly - I'm not sure about train connections. We've taken the ferry between Split and Dubrovnik on a previous trip and it's very doable. Have you looked at the possibility of flying from Split or Dubrovnik to Athens? Lots of options!!

How long does the ferry take? I took a bus between Split and Dubrovnik - they run all the time and are very inexpensive. If I remember correctly, it took about 4-4.5 hours. Plus great scenery on the way.

Spike, I traveled to Greece and Croatia this past June. In our case we flew from Athens to Dubrovnik (flights on Tuesday and Sunday at 7pm). From Dubrovnik we took a shared van to Korcula and then a ferry to Split. You have several options from Split (rent a car, rail, or bus to Zagreb). You could also do the route in reverse. Note: going from Dubrovnik to Korcula the ferry only runs on Thursdays. Good luck

Jon, Thanks for your input. After more searching and the work of an agent we were able to book flights from Athens to Dubronik $600 for 2--Thursday and Sunday. Since Dubrovnik is our main interest this was attractive. It cuts out Zagreb and taking a train. We willl have 7 days for Dubrovnik and Korcula. What was the advantage of the shared van to Korcula. Would we just as well off to stay all seven days in Dubronik and side trip to Korcula? When we arrive in Athens we have a full day before going to Dubrovnik. Is it convenient to stay in Athens that night and going back to the airport. After Dubrovnik, ee plan to ferry to Mykonos and Santorini and fly back to Athens for our return. Any thoughts are welcomed.
Spike

We have visited the Dubrovnik area twice and both times have slept in Cavtat, a lovely little fishing village about 5 minute by bus from Dubrovnik (close to the Dubrovnik airport). It's easy to get into Dubrovnik to see the sights (via bus or boat) but then you get to escape back and sip wine along the harbor while you watch the yachts dock in the sunset. Beautiful place. I would spend 4 nights in Cavtat or Dubrovnik and 2 nights on Korcula. I've never done the shared van but it sounds like a great idea. Depending on what time your flight leaves for Athens, you may or may not be able to get back from Korcula to the Dubrovnik airport in time. You may need to spend your final night back in Cavtat (or Dubrovnik). I don't think you can do Korcula as a day trip.
Here's a website that can show you all the cruise ships in port in Dubrovnik on a specific day. http://ports.cruisett.com/schedule/Croatia/184-Dubrovnik/September_2013/ Schedule your day trips accordingly. I would recommend highly that you go to Montenegro. You can rent a car and drive yourself or take a tour bus (I think it's Atlas). I've never been to Mostar but others highly recommend it. Regarding the Athens airport, if you have most of a day, you should spend it in Athens. Whether you sleep in Athens or near the airport depends on how early your flight is. Search the Helpline for "Hotels near Athens airport". Hope this helps!