It appears that you are planning to do Athens then Crete. Since you are arriving Athens mid day you will have time to catch a flight that day to either Heraklion or Chania Crete.
By the way Aegean Airlines just announced a 50% off sale today. Good time to book flights. Aegean is a star alliance member. If you book your transatlantic on a Star Alliance member you can probably get the connector on one ticket which can be helpful if for some reason you do not make the connection.
You will want to do Crete first because it is South so it will be a bit warmer and gives you time for Athens to get a bit warmer later on.
On Crete you are going to have to cut down on the places you want to go. Its over 400 kilometres long and you have mentioned places on either end of the island.
If it were me I would fly to Chania first. It is delightful with its walled old town and Venetian era harbour. When you wander the streets of the old town it is easy to pretend you have stepped back into the 14th century. Its a great place to get over jet lag. Be sure to book a hotel in the old town.
You will not need a car until you are over jet lag. You will have no use of a car when you are in the old town. You can check into excursions at any travel agent. You will find the travel agents just outside the old town. They can arrange wine and olive oil tasting.
We used Smart tours. A few years ago they had small group tours by mini bus that included winery tour and oil and wine tasting.
we stopped off at their office at the bus depot but it was closed. Its probably best to contact them through the web site.
If you want to see Balos you need to check to see if the day excursions are running. They include pick up and a bus to Kissamos and a ferry to Gramvosa to see a ship wreck and a 14 century ruined fortress. The ferry will continue on to Balos. I think it might be too early for a beach oriented day trip.
Elafonissi can be done in a long day trip by car. The road south is winding and hilly. Again it may be possible to take a bus check the KTEL bus schedule to see if they are doing that day trip.
You probably would be interested in Ancient Aptera just 18 KM east of Chania. It has 5,000 years of history with most of the ruins from the Roman period.
After Chania head east and visit Rethymnon. It too has an harbour and old town area. Its well worth a stop on the way to Heraklion. Be sure to visit the giant Venetian era fortress across from the harbour.
30 km east of Rethymnon you might want to visit Melidoni cave. Its a large interesting cave. There is a sad history associated with this cave.
In Heraklion you will want to visit the Archaeological museum. It has most of the artifacts found in Knossos. Do that before you visit the site. Heraklion is a very busy city. The central area is quite nice. It too has an old town area that is great to wander around. Find a hotel near the waterfront (I can recommend Kronos) That way you can see the ocean and stroll into the central area easily. Be sure to joint the evening promenade when everybody wanders around the old town.
After Knossos on another day you can drive south and visit another Minoan ruin at Phastos. Unlike Knossos it has been excavated but not rebuilt. For a real gem, continue south to the Roman capital of Crete Gortyz or Gorten. There is a gated site there which is interesting but the adventure begins after you leave the gated site. Walk directly ahead down the road from the parking lot. In a couple hundred meters look to the left through the olive groves. There is a partially excavated Roman city in those olive groves.
That might be the highlight of the trip .
I respectfully suggest you concentrate on the west and central areas. Leave the east part of Crete for your next visit.
I will post pictures of the areas I have suggested on the next post as I have run out of room on this one.
