Spain - Madrid then San Sebastian

Planning on a 9 or 10 day trip to Spain, likely in late May or Early June. Trying to avoid peak crowds but still have warm enough weather.

By way of background, we certainly want to see the main sites and will do a museum here and there, but food is very important on our trips. We also prefer to stay a little outside the most touristy areas and get at least a little sense of the local culture.

Fly into Madrid. Was thinking 3 nights there is penough? Was looking at a hotel in the southern Chamberi area, which seems to fit what we like?

Our flight lands at 7 am (ugh). Plan to drop off the bags and then found a 2.5 hour, well reviewed, "Welcome to Madrid" small group guided walk. I like to do something like that on day 1 as it helps get the lay of the land. Will do a Prado highlights tour the next day. I always find the "skip the line" tours to be well worth the added cost. Other than that, planning on wandering around and eating and drinking. Open to any restaurants or sites we must see or tours would should do (we only do 1 tour a day, we like a morning tour then explore the afternoon).

Then onto to San Sebastian for 5/6 nights. How to get there? I see there is a train but it is 5.5 hours minimum. Fly a better option? I'd also be open to a private driver if it didn't cost a fortune. Planning on staying at the Hotel Maria Cristina, but open to options. I know 5/6 nights in a such a small town is a lot, but we intend to do 3 full day side trips. Was thinking:

-French Basque country day. Hit 2 or 3 towns, lunch in one of them
-Bilbao, Getaria, with a stop at a Txaoli winery or cider house
-Rojas winery tour with a lunch stop in LaGuardia

Open to other options and ideas. Probably do a small group tour for 1 and a private tour for 2

Also, would like to do 1 or 2 of the Michelin starred place in San Seb. If anyone has tried any of them, let me know. Don't want a fancy place everyday as I want to eat a 1,000 pintxos, but would like to try at least 1. Very open to any restaurant options or other things to do.

I generally only like to stay in 2 different places as the packing/unpacking gets annoying and packing light is not in my GF's vocab. But open to it if there is somewhere we just must also stay.

Thanks