Chania is a great choice. A wonderful charming town. Elounda is great for a quiet laid back stop, Agios Nikolaos has a more interesting vibe and is more of a real town. Also very charming. I prefer Ag Nik but Elounda has more luxurious hotels. (Crete hotels.) Naxos has lots to see in the interior so if you didn’t explore then certainly consider that. Folegandros and Milos are both incredible. Folegandros is more suited to walking and relaxing (and has some top notch restaurants and hotels). On Milos you need to do a tour and get out and actively explore to do it justice. Geologically Milos is stunning. A little like Santorini but with better beaches.
You seem to have your heart set on Zakynthos but I have to say it’s not a good use of time for a sort-of overrated payoff. Your time is much better spent (in my opinion) seeing another Greek island in the cyclades (maybe taking a ferry to Naxos or Paros sitting outside on the deck drinking a bottle of wine) rather than taking a bus and connecting flights. Zakynthos and Santorini/Mykonos are on opposite sides of the country and the only way from one to the other is by flying (or some combination of bus and ferry). So, my recommendation is to consider spending those Zakynthos days in Naxos, Paros, Milos, or some other Cycladic island.
With so much on offer, choosing where to go island hopping along the Adriatic Coast can be tough. Maybe you want gastronomic delights, perhaps you want to party all night long? Or it is that you simply want a sandy beach? Do you want to sail to the islands or ferry from mainland? The various and varied Croatia islands offer culture, nightlife, history and of course relaxation. Find out which one is perfect for you in this Croatian islands guide.
Can you see all the major sights in Athens in one day? No. But you can see the Acropolis, Acropolis Museum, and the top historical sites of the Plaka in one day. If you had an extra half-day then visit the Archaeological Museum in Exarcheia. That still leaves many great sights but you will have seen all of the iconic Athens attractions. Adding Naxos is always a good idea. You might even enjoy it more than Mykonos (but no nightlife like Mykonos).
The Greek islands have beautiful weather in the months just before and after peak season. It’s a great time to see the islands, save money, avoid the crowds, and still have great weather (though not as hot as July and August). If you want to see the super-popular islands of Santorini, Rhodes, Corfu, and Crete without the tourists then this is a great time to visit.