Crete - some help fine tuning my vacation needed!

Hello!
I'll be traveling with my fiance to Crete in a couple of weeks - to spend 4 full days in Crete.
We were thinking of getting a rental car and stay in Chania.
The plan (of the full days) is:
day 1 - Going to Balos Beach, along with the adjacent island.
day 2 - Doing the Samaria Gorge hike
day 3 - go to Elafonisi beach
day 4 - still blurry. We need to finish the day in Heraklion because we have a flight in the morning afterwards.

Help needed in the following:
1. How should I get to Balos? I read that using a ferry is the best way. Do I need to book it in advance? which company should I choose? Can I use my rental car in anyway?
2. How should I go about the transportation? is it easy to handle it on my own (using a bus on the way there, and a ferry and another bus the way back, is what I understood so far), or should I use a tourist agency?
3. Chania-Elafonisi and back - Any beautiful village, winery or anything else I can stop by which is pretty much on the way? Is Manousaki Winery worth the detour?
4. I would love some help. So far I gathered the following "stops":
a. Seitan Limania Beach
b. ancient Aptera
c. Lake Kournas
d. Rhethymnon for a tour of the city and lunch, and then
e. Sacred Monastery of Arkadi

Is it too much to try and shove them all in one day?
What should I lose?
Any other changes?

Thank you so much!

For Balos, the easiest way will be to drive to Kissamos paort (after Kissamos town) to get the boat trip, you can book online, depending on the season there are either 1 or 2 companies doing the trip.

from Chania for Samaria gorge you can either buy a ticket with a tour agency (you can get it the day you arrive in Chania, Halidon St & around there are many small tourist offices, all offer the same trip). Or you can just go on the public bus & ferry from the central bus station. I assume you are aware it is an 18km, long, hot, difficult hike, with the 1st 2 km down uneven wooden stairs & the rest on stony rough paths? You need good walking boots & most people like to schedule a quiet day the following day.

Elafonisi is just under 2 hours drive from Chania. It is nice to drive through Topolia gorge (you can stop to see the cave church of Agia Sofia) & back around the coast. Or go via some of the traditional villages, like Elos & Kandanos, particularly important if you have any interest in WWII. Or detour to the eco-village of Milia, only if you like long drives on tiny dirt roads! an amazing place. At Elafonisi, Do walk across to the 'island', you may need to wade through the little channel, as that is where the beach is prettiest & pinkest. I recommend going early in the day as the beach gets full by midday.

Don't forget to give yourselves a minimum of 1 day in Chania itself, a wonderful ancient city, stroll around the Venetian harbour & many tiny alleyways etc.

You could stop off at Aptera & Rethymno on your way to Heraklion, that is probably plenty for 1 day. Seitan Limani is the opposite direction & not easy to access. Or go to Heraklion earlier to see the modern Archaeological museum.

Not quite what you asked, but perhaps a different suggestion. Ditch the car and take the bus to the entrance to the Samaria gorge. At the end, stay the night in Agia Roumeli. The next day, take the ferry to Palaiochora and stay the night there. It's a nice little town. You could do Elafonisi beach the same day, there will be time.

The next day, head back to Chania and slowly make your way to Heraklion, stopping and checking out various towns along the way.

Yes, you'll miss Balos beach, but you will have spent the day at Elafonisi which I think is nicer. You'll see more this way and you hit everything on your list, minus Balos.

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