We booked a great tour in Athens on our own with Greece Cruise Excursions you can customize it if you want and you set the pace so we didn't feel rushed at all. LOVED the tour!
We just came back from many of those places. My strongest recommendation would be regarading Ephesus. A friend recommended a private tour. Just email Denizhan [ephesustours@yahoo.com]. Our guide was Orchun. Very good. This was affordable and very good. Best decision of the trip.