Lillie,
It's great that you're starting on your planning now, as it allows lots of time to work out the "fine details" (with help from the group here of course).
To begin with, I'd highly recommend that you read Rick's Europe Through The Back Door as it provides a LOT of great information, including Itinerary planning, transport options, lodgings, etc. Also, Rick holds Travel Festivals twice a year in Edmonds (usuallly Feb. / Mar.), and that would be an excellent time to gather information on the destinations you want to visit. It's also a great opportunity to speak with LOTS of experienced travellers - be sure to bring a note book and pen! There are also courses held at Edmonds throughout the year, usually on Saturdays. Check the main page of this site.
Also, could you confirm that your trip is only two-three weeks long (mid May to the first week of June). That will have a definite bearing on how many locations you can reasonably visit. One common trend, especially with "first timers", is an unrealistic expectation of how many cities they can visit in a specific time frame.
Could you confirm where you want to visit in Greece and for how long? If you only plan to visit Athens for a few days, I'd be tempted to drop that given the fact that Greece is a bit "distant" from your other destinations.
Using "open jaw" flights would be a really good idea, but you won't be able to buy tickets just yet. The tickets for May/June '09 probably won't be available until later this year. You'll need a fairly good idea of which cities you'll be visiting before you can work out the transportation options.
Once you have more a more specific Itinerary worked out, it will be much easier to provide more detailed information for you.
Hope this is some help?
Cheers!