Need itinerary feedback/second trip to Spain

As part of a 3-week trip to Spain, we spent a week in Donostia/San Sebastian, Hondaribbia Hendaye(France) and Olite. I really like your #1 Itinerary because you’ll see some of the coastal towns between San Sebastián and Bilbao we missed due to time. Mundaka, Getaria and Lekeitio looked really appealing from the research I did. Some are located at the very end of the road so it can take 20-30 minutes to drive to one town and then 20-30 minutes returning to the main highway. As it turned out, we had great weather in San Sebastián and had great beach time there and bodysurfing at Zurriola’s beach right next door to Donostia/San Sebastián.
You might consider taking your rental car from HONDARRIBIAinto the French Basque villages of AINHOA and ESPELLETE before crossing back into Spain and visiting the Village of URDAX and the CAVES OF URDAX nearby. We did this all in one day before arriving at OLITE. We stayed at the incredibly huge castle in Olite. which today is a historic Parador. When we drove into town, there were throngs of people dressed in red and white because it was the weekend of the wine harvest festival in September! OMG was that a fun experience! Complete with bands playing in the streets and even a mock bullfight in the town center. ( The bull was unharmed during the event). The next day we drove to ELCIEGO, where the Bodegas Marques de Riscal winery had Frank O.Gehry design their new hotel with the signature Frank O. Gehry architectural style. . Before seeing Gehry’s famous Guggenheim creation in Bilbao, Elciego is a gem.
Then it was on to the Bodegas Ysios in LaGuardia— a remarkable winery at the base of the Sierra mountains. The building looks like a moving wave and was designed by renowned Spanish architect Santiago Calatrava.
Having a car for a couple days here and there really made visiting the Basque Country a wonderful experience. You can discover places not even on the radar when you’re planning your trip and spontaneously park and explore on a whim.
And everything said about the fantastic food and wonderful Basque people is true.
Have a great trip!

Great plan, but consider exploring the Bordeaux region of France for a few days on your way from Paris to San Sebastian.

Some comments on your itinerary, as a Bilbao-born local:

Itinerary 1
-Train to San Sebastian (San Sebastian/4 nights): One day for Hondaribbia, and two full days for San Sebastian (or one day for San Sebastian and another day trip).

Bus is also an excellent option, most US visitors tend to ignore this great way of moving around in Spain. Sounds good, Hondarribia (not Hondaribbia) is easily accessible from Donostia-San Sebastian, on the way there I would try to stop in Pasai Donibane (aka Pasajes de San Juan).

-Rent a car and do a scenic drive along the coast to Bilbao. Possible stops at Getaria, Zumaia, Lekeitio, Elantxobe, Mundaka, Bermeo, and San Juan de Gaztelugatze (I'm not picturing stopping at each place, but rather picking one or two when we want to stop and eat or something catches our eye. San Juan de Gaztelugatze, however, is a definite stop). Is this a realistic plan with my stop-and-smell-the-roses husband? A more direct route looks to be about an hour, but I don't know how to estimate how much time a coastal drive would take.

Bear in mind that parking may be complicated in most of this towns, at least from June 1st when parking restrictions start in many of these places. It´s practically impossible to park in Lekeitio town center, you have to park a mile and a half away, and it´s always metered and very limited. Elantxobe is also quite complicated, as it´s a very steep town with few available parking spaces, you need to walk a long way to get to town. Same for Mundaka, sorry! Bermeo will be easier at the very far end of the port. San Juan de Gaztelugatxe may need a previous reservation if you want to hike the 241 steps (but to get to the steps you need to get to sea level first, on a steep descent).

-Arrive in Bilbao and return rental car (Bilbao/6 nights): Day trips to Vitoria-Gasteiz, Guernica, and Getxo. Two full days in Bilbao. (Or may drop a day trip and do three days in Bilbao.)

Plentzia, very much ignored by foreign visitors, is also a must (last stop of our subway system, very practical once in Bilbao. Cheap, safest, cleanest, very efficient). In Gernika you must absolutely visit the Assembly House (Casa de Juntas, need previous reservation, one of the oldest Parliaments and forms of democray in the world, still our government), one of the reasons John Adams (with John Quincy and Richard, his sons) stayed in Bilbao for 9 nights in 1780. In Getxo, the unique Puente Bizkaia is a must (accessible on the subway), as well as the old port of Algorta (I live in this town).

--OR--

Itinerary 2/Remove Castilla y Leon.
-Add in overnights at Vitoria-Gasteiz and do day trips to Pamplona, Laguardia, Logono (wine-related activities are not of interest to us, so I haven't researched this area too much) and/or other places.

The underground cellars of wineries in and around Laguardia are a must, even if not interested in wine, back to 14th century and still working. Logroño is not that interesting (and do not mistake La Rioja with Rioja wine region, two different things). Vitoria-Gasteiz is the capital of the Basque Country and offers a beautiful old quarter, as well as a great visit to the reconstructed Santa María Cathedral, "Open For Works".

-Additional day trips from San Sebastian and/or Bilbao.

Durango, Elorrio, Balmaseda...from Bilbao; Oñati, the sanctuary of Arantzazu and basilica of Loyola (this last one, where the Jesuit order started), Tolosa, Segura, Orio,...

Hope this helps! Roads are in very good condition, but it´s a wet and rainy area, plenty of mountain roads and beautiful landscapes, like a little Switzerland (well, here we tend to say that Switzerland resembles the Basque Country!)

(Kenko´s suggestions are also very good, of course! But you will not be here during wine or any other festivals, at least any I can recall now).

Based upon the feedback, I think we will focus on Basque Country only in Spain, and research whether we should add some additional exploration in France.

Thank you for the input.