Need help with itinerary - Northern Spain and Greek Islands - 3+ weeks

In my opinion the most common route for hopping island is Santorini - Naxos -Paros .
The compact ferry goes from the port of Pirea- Paros 4hours Paros- Naxos 1 hour and Naxos-Santorini 2 hours

Santorini is a must.
Naxos is the biggest island of Cyclades with many traditional hilly Villages and nice beaches ideal for family vacations
Paros is much smaller than Naxos and combine everything. And although, it’s not so famous as Mykonos and Santorini, bus it has one big plus! It’s for everyone! It has beautiful beaches, sport activities, trendy bars and clubs, tasty food, wineries, traditional architecture, paths for trekking and hiking etc. The list as you might understand goes endless. It is the perfect destination for both families and adventurous travelers. That’s why if you go to Paros, you notice the variety of ages that visit it, from young people and students, to families and older couples. This creates an amazing mix that gives this island an extra dimension!

In Paros & Naxos you can expect attractive prices for accommodation compared to Santorini and Mykonos

You can visit my blog about Paros
https://captainsandrewhideaway.wordpress.com/

If I am reading this correctly you have about 5 weeks but most of this trip is going to be in October returning October 29.
It appears you are planning three weeks in Greece. Correct?
I take it Santorini is definitely in your plans. Are you flying directly there or connecting in Athens? Where do you flan to fly from to get to FCO. Late October can be a great time to be in Greece but the season is definitely starting to wind down. If you could give us just a bit more info on what you are hoping to get out of this trip and how you plan to arrive and depart we can probably give you some good information.

Sorry for not being clear. We plan 2 weeks in Northern Spain - 9/24 - 10/8, then fly to Greece from either Bilbao or San Sebastian.

I am not sure where in Greece to fly into; Athens, Santorini, ??. We will be in Greece from 10/8 to 10/28. Will need to fly from Greece to FCO on 10/28 to depart to LAX the next day.

I'd love to visit Athens, Santorini, Naxos and Milos, maybe Paros, too. Is it best inter-island flying or via ferry? How long should we stay in each, what is each place specifically that is a must see... Do we start our adventure in Athens or? What is the most practical and budget friendly itinerary?

Thank you for your time and advice.

You will probably have to fly to Athens. I just did a search for Santorini to Rome and there are no direct flights on October 28. So that means you are probably going to have to fly in and out of Athens.
Most experienced travelers like to get out to their furthest island immediately on arrival in Athens. We take the first connecting flight and leave Athens to the end of the trip. It appears you are interested in Santorini Naxos Milos and possibly Paros.
Sequence is important when island hopping and every hop eats up a minimum of half a day. Fortunately you have lots of time.
Options
Crete may be a consideration for you. It has lots of Ancient sites Minoen to Venetian to Roman. It has great beaches. And it is so large that you can easily spend two weeks there and just visit the west. It is relatively inexpensive for hotels and dining and can be done on a modest budget. Transportation by local bus is cheap and reliable.
Western Crete http://www.flickr.com/photos/stanbr54/sets/72157632115757899/

Aptera images 38-62 Balos Gramovossa images 79-106
Crete Archeological sites https://www.flickr.com/photos/stanbr54/sets/72157645085297380/
2017 Crete Archeological sites. https://www.flickr.com/photos/stanbr54/albums/72157691001013665

There are several daily ferries from Heraklion to Santorini which takes about 2 to 2.5 hours. Santorini is expensive for food and hotels but It is amazing for its caldera views. This is the place to splurge and get a hotel with Caldera views. Probably three nights is enough.
Santorini http://www.flickr.com/photos/stanbr54/sets/72157632154800782/

If you have chosen to do Crete then you probably will want to fly from Santorini and end your trip in Athens. Three or 4 days in Athens is enough to see the major sites. get a hotel near the Acropolis and everything important will be within walking distance.
Athens http://www.flickr.com/photos/stanbr54/sets/72157632121475515/

If you have not chosen Crete then fly to Santorini or Milos. If you really want to do Milos you have to plan carefully. Its not on the regular Cyclades ferry routes. As far as I can see there is only one ferry a day from Milos to Naxos and that takes about 6 hours. So if you can get a flight fly to Milos first. Milos will be fairly quiet at this time of year as the season winds down quickly after August
Milos http://www.flickr.com/photos/stanbr54/sets/72157632109429236/

Spend your time in Milos then take a ferry to Santorini. There are more ferry choices on that route. From Santorini there are lots of ferries that do the Ios, Naxos, Paros routes. Naxos is our favourite island and needs a minimum of a week and you won't be able to see all it has to offer. 10 days would be even better. Stay at St George beach. Its part of Naxos town so you get a beach vacation with all the activities of town. All of this just a 10 minute stroll along the shore to Naxos town waterfront promenade. Naxos has a smattering of antiquities, great beaches, hikes and mountain villages where you can see what life in Greece was like in the past. You can also take day excursion boats to Delos Mykonos or the small Cyclades islands. Of course Paros is equally as nice so you can do both in two hops or just concentrate on one.

Naxos Mountains and Villages http://www.flickr.com/photos/stanbr54/sets/72157632110674306/
Naxos Town http://www.flickr.com/photos/stanbr54/sets/72157632094558042/
Trip around Naxos http://www.flickr.com/photos/stanbr54/sets/72157634605629689/
Fly back to Athens for the end of your trip. There are no inter island flight to these islands it has to be done by ferry but all of them have flights to Athens.
Hope that helps

Dear Stanbr,

Your advice is amazing! Thank you! I'll need to digest the information for a bit and probably will come back with questions/clarifications.

I already have the airline tickets LAX-MAD/FCO-LAX. This is because we originally were going on a cruise that ended in Rome. My husband worries about missing flights, so he wants to be in Rome on 10/27 to ensure we return home on 10/29 at 8:15 am. This means we have 19 nites, 18 days in Greece.

Crete sounds wonderful.. Would you recommend Chania or Heraklion airport? Recommendations on where to stay?

Is this the best sequence? And please clarify Ferry or fly in between islands?
Athens - Crete
Crete - Santorini
Santorini - Naxos
Naxos - Milos
Milos - Athens
Athens - Rome
Rome - Los Angeles

Thanks!

I agree with your husband be in your departure city at least a day before your return flight.

I would fly into Chania airport and do Chania and west Crete. To get to Santorini you will need to take the ferry from Heraklion so leave Heraklion till the end of your Crete trip.
You can easily spend a week in West Crete. Chania old town is amazing. Stay right in the old town. We stay at Theotokopoulou street. Its pedestrian only just a block from the Venetian harbour so you have access to everything important but just far enough away to be quiet at night for sleeping. Theo street has hotels in every class and price range. We are budget travelers and stay in Studios and have been staying with Natalie at Pension Nora for years.
Chania http://www.flickr.com/photos/stanbr54/sets/72157632117917828/
Theotokopoulou St area http://www.flickr.com/photos/stanbr54/sets/72157632118491316/

You might want to take the early bus to one of the south coast beach villages perhaps Paleochora or Sougia. Even in October these villages are still active. You might want to take the ferry trip along the Lybian sea. Its a wonderful trip.
Ferry trip Libyan Sea https://www.flickr.com/photos/stanbr54/sets/72157653434073393
Crete Libyan Sea villages https://www.flickr.com/photos/stanbr54/sets/72157645487373222/
I think you have Santorini and Naxos nailed however as I suggested earlier Milos is goin gto be a problem on your proposed plan. There is only one ferry that dies that Milos Naxos route and because it is now basically off season that ferry is not in operation this late in October. So the only way you can include Milos is to fly directly there then take the ferry to Santorini but then you will have to take a ferry to Crete, then return to Santorini by ferry to take the ferry to Naxos.
In my opinion that sequence just makes no sense. So I would drop Milos entirely it just totally complicates everything. If you must do Milos then you will need to fly there and fly back to Athens then fly to Crete.

You are going to have a much nicer trip by dropping Milos and adding that time to Crete and Naxos. Greece is a place where less is more.

I agree with Stanb that you should skip Milos for this trip. I was just there and while I really enjoyed it, it wasn't any better than Paros which you could more easily do in connection to the other places you are going. Starting in Crete ( 7 nights), ferry to Santorini (3 nights), ferry to Naxos (3 nights), ferry to Paros (3 nights), ferry to Athens would work.

Here is a trip report I did from a trip that included Santorini, Naxos and Paros - https://www.fodors.com/community/europe/from-santorini-to-the-peloponnese-isabels-photos-and-trip-report-801531/

Here's one for Crete: https://www.fodors.com/community/europe/a-week-in-western-crete-with-photos-1135170/

Here's one for Northern Spain - https://andiamo.zenfolio.com/blog/2017/9/crisscrossing-the-camino---5-weeks-in-northern-spain-part-3-san-sebastian-to-santander

And photos of all those places are here: https://andiamo.zenfolio.com/