This is all so wonderful, thanks. I think the first part has mostly come together. What do you think of the second half?

Toledo
Fri: Hospital of Tavera, Church of Santiago del Arrabal, Zocodover, Hospital of Santa Cruz, lunch at Coleccion or Asador, Cathedral, Ayuntamiento, Santa Isabel de los Reyes
Dinner: Kumera.
Sat: AM: Begin tour at Plaza de San Andres, San Lucas, Taller del Moro, Church of Santo Tomé, Lunch: Restaurant Cafeteria Carolvs, PM: El Greco Museum, Synagogues, San Juan de los Reyes, Dinner: Casa Ludeña

Madrid
Sun AM: arr Madrid
11AM: Habsburg Walking Tour (snack on tapas after Royal Palace)
Lunch:
PM: Museo Thyssen-Bornemisza
Tapas: Plaza Santa Ana

Mon
AM: walk the Castizo Quarter
Lunch: Mercado de la Paz
12PM: Museo del Prado
Calle de Arenal & Plaza de Isabel II
Wander/tapas in Cava Baja area

Tues
Day trip to Segovia
Aqueduct, Cathedral, castle
Lunch: Jose Maria?

Weds
9AM: Sofía National Museum
Buen Retiro Park
PM: walk Gran Vía, Malasaña & Chueca
Sunset: Templo de Debol

San Sebastain
Thurs Arr in PM, Dinner in Gos area
Fri Aquarium
Hike Monte Urgull
Lunch in Parte Vieja area
Museo de San Telmo
Palacio de Miramar for gardens
Dinner in Centro area

Sat Museo Chillida-Leku
Kursaal
Wander old city center
Dinner in in Parte Vieja area
Be Bop for jazz

Barcelona (5 nights)
Walk La Rambla, ½ Day trip to Sant Sadurní d’Anoia (Cava), Walking tour of Gothic Quarter, Walking tour of El Raval (museums), Walking tour of L'Eixample, Walking tour of La Ribera, Lunch: El Roure for paella

Thoughts? Major places I'm missing?

Sounds great! Just a couple of comments on the San Sebastián plans. The Chillida-Leku Museum is regrettably temporarily closed, and Be Bop bar is not always jazz; often soul, blues, funk. But anyhow a great place!

Good to know about the museum being closed. And any music is just fine by me, but thanks.

Do you think there is time in the San Sebastian portion to venture out somewhere into Basque Country? Maybe a 1/2 day trip? I don't want to miss a single eating opportunity in SS, but wondering if I'll get a little bored considering what the weather will likely be.

Did you end up with 3 nights in San Sebastian? If so, then this will probably just be 2 full days by the time you factor in the travel time. You probably won't have time for a daytrip. But you could have a couple of ideas handy in case you end up getting the energy for one (and depending on the weather). Hondarribia is nice as is Getaria. But if you are flying into/out of the Bilbao airport you could always incorporate a daytrip to Bilbao. I wouldn't worry too much about planning out specifically where you're going to dine for the trip (unless the place requires reservations). This way you can be more spontaneous.

I need a nap just reading this.

No chance whatsoever to get bored in San Sebastián in three days, regardless of weather.

But there are plenty of options for great day trips, both inland and along the coast. Great public transportation. A few miles inland you have places like Tolosa (the best steaks in the world, and famous for its "Alubias de Tolosa, a local been dish) and the medieval university town Olite: http://www.oinati.eu/turism/turism?set_language=en

Along the coast towards Bilbao you have lots of fine small villages such as Getaria, Zumaya, Debea, Mutriku, Lekeitio etc. Of course fabulous food here also.

Fantastic fish and seafood in all of the restaurants down in the harbour area in tiny Getaria just west of San Sebastián. Had the meal of my life here, something like this: http://thepauperedchef.com/node/255

I also always take first time vistors to the area to a lunch in pictoresque Donibane/San Juan some 5 km east of San Sebastián. Excellent seafood restaurants at the waterfront with great value three course lunch menus with wine included for some 15-20€. The local fish soup is to die for. The bus leaves from Plaza de Guipúzcoa in Central San Sebastián about once an hour and takes some 30 mins. You can also walk here in a couple of hours along the coastline, includes a smalll boat ride from San Pedro to San Juan, takes 2 mins and leaves all the time. http://www.euroresidentes.com/eurore...s/san-juan.htm

Restaurante Txulotxo: http://www.restaurantetxulotxo.com/index.html

All six restaurants in Donibane: http://www.etxekar.net/donigastronomia.html#

In San Sebastián I also recommend the newly renovated San Telmo museum at the outskirts of the Parte vieja/Old town, dealing with Basque history and culture.
http://www.santelmomuseoa.com/index.php?lang=en