You will fly to Santorini on day of arrival in Athens. You will need at least 2 hours to make a connecting flight. Athens airport is very efficient with arrivals and departures n the same building.
Your transfer from Santorini to Chania is going to use up basically a full day as the ferries arrive Heraklion around 7 in the evening and then you will have to take the KTEL bus to Chania which will take about 2.5 hours from ferry arrival. You will arrive Chania in the evening.
You might consider flying back to Athens from Santorini and connecting on a flight to Chania. We did that once and were in our Chania hotel before noon.
The same logistics problems arise on your transfer from Chania to Athens. Find a morning flight so you are in Athens and in your hotel before noon.
There are excursions from Chania that can be booked from any travel agent near the old town and harbour. See if you can contact Smart tours. They used to be located at the KTEL bus station but when we went there in May the office was closed. Try contacting them by internet. They have small bus tours no more than 12 people. We took a wine and olive oil tasting tour just before covid. It was inexpensive and a really great experience.
You can also look for an excursion to Kissamos for a visit to Gramvossa and Balos lagoon. While not actually a tour you do get a pirate fortress a great beach a decaying ship wreck at Gravossa and a wonderful beach and mountain views at Balos.
In Athens there are tours of the Acropolis and day tours that can include Delph and Meteora perhaps Nafplio as well for 2 or 3 days. Thats really all the time you will have because central Athens takes 3 days to do nicely.
Here are a few photos to whet your appetite.
Delphi and Meteora https://www.flickr.com/photos/stanbr54/albums/72157698930270992
Gramvousa,Balos and Elafonissi https://www.flickr.com/photos/stanbr54/albums/72157698932695812
Return to Chania 2022 https://www.flickr.com/photos/stanbr54/albums/72177720299646015
