Spain in September - 2 weeks - Finalizing Plans!

Only comment is that of the 12 days on the ground, 25% of them are travel days - which means you will have little time to enjoy the area once you factor in travel time, checking out and checking in, packing, unpacking, etc., etc, Remember, each change of location will take up 3/4 to a whole day. Obviously only you can decide how you want to allocate your time and what trade -offs make the most sense to you. Personally, with only 12 days on the ground I would take Menorca off the plan and focus more on the other three areas you have listed.

San Sebastián, Cadaques, Menorca - all far flung involving long (and complex) travel days. With a total of just 13 nights, I would choose either Cadaques or Menorca, not both.

How do you feel about museums? I think Bilbao is a solid day, between the museums and the Cas o Viejo (historic distict). Since you're basing in San Sebastian, I assume yoj have a out a day's worth of activities there.

I don't believe you can comfortably cover all the other Basque Country targets on Sept. 7, much less La Rioja. I don't know how long the coastal route between SS and Bilbao will require. The most direct route doesn't follow the coast for most of the distance, and that's estimated at about 1-1/4 hours by Google, which tends toward optimism. In fact, Google routes you through Bilbao to go from SS to San Juan de la Gaz. and estimates 1-3/4 hours, and you're still not fully following the coast (not passing through Lekeitio). It appears that the coastal drive alone will be quire time-consuming even if you make no stops, and Hondarribia is on the other side of SS.