Help requested for travel planning in Spain

Eurail is not a type of train. It is a company in the US that sells passes on and tickets for european trains - at a premium so they make a profit. Each country has it's own train system and will sell tickets for less, sometimes considerably less. Usully you can buy tickets after you arrive (except for overnight trains which may sell out far in advance).

IMHO you are better off doing Adalusia (Seville, Granada, Cordoba and perhaps one of the White towns all at once while staying in the south. We always do it by car - which is much more convenient - and probably not much more for 2 people, but definitely more epenisve for 1.

Trying to give some ideas re. your different time slots. By no means a full summary of options.

Day trips from Madrid (besides Toledo)
El Escorial
Aranjuez

Andalucia
check www.renfe.es (Spanish Rail) for web fares. They can be pretty low when you book in advance.
You can go by train to Sevilla, bridge the distance between there and Granada by car (to see some of the White Villages, which are at least as much a "must see" as the 3 major cities), and go by train back from Granada to Madrid.

Barcelona.
No, 3 days is not too much. You'll have a truckload of sights, architecture, museums to see. One side trip could be Montserrat monastery.
Vueling is a budget airline that goes to BCN, but you can check whichbudget.com for more option, and compare with renfe's rail prices (highspeed train connection can beat the plane when you compare door-to-door travel times).

The remaining 3 nights
Well, you must have had a lot of heat until now, so either go North (San Sebastián, Bilbao, Galicia, Santiago de Compostela), or - when not against another flight and prefer a more urban destination - to Lisbon.

As suggested see the other areas of Spain which are quite different than Madird. But also learn to live like a Madrileno in terms of eating and their times for eating, visiting the Retiro, or going to the Rastro and the stamp vendors at the Plaza Mayor on Sunday mornings.

learn in advance what holidays may be taking place and participate.

Agree with Cowboy that 3 days is not too much in Barcelona.

We used Vueling last year from BCN to Granada. Good cheap tix, though they nickel and dime you for everything (seat reservations, luggage). Nonetheless a good deal and good way to go from north to south quickly and easily.

I love Salamanca! Really nice university town, charming Plaza Major, small enough for a short visit and close to some other interesting towns (Avila is probably the most well known). Also, once you're there, you're not too far from Portugal... maybe 2 hours to beautiful Coimbra, less to the border.

It will be hot as hell in most of Spain.
I would travel by train from Madrid to (stop in Cordoba ?)Seville, bus ( or drive)to Granada from Seville ( 3 hours).
Barcelona is a great place to spend even more than 3 days. I would not go much further - you can take a day trip to Girona or spend a day at the beach ( Sitges).

To help you guide your way through the WHS of Spain here is the list.
http://whc.unesco.org/en/statesparties/es
I would suggest a rethink to include a few more and at the same time "localize" your journey.

Perhaps I missed it, but don't see Segovia mentioned. It is a great day trip from Madrid.