Place to stop on way from Barcelona to Madrid.

Your best option would be Zaragoza, which is a city that lies halfway on the AVE high speed track from Barcelona to Madrid.

Zaragoza has more than 2,000 years of history including Roman ruins of the city walls, forum, and amphitheater, as well as the Aljafería; an 11th-century Moorish palace. It's also the home of the famous pilgrimage site of Nuestra Señora del Pilar Basilica, housing the miraculous image of the Virgin Mary of Pilar. The best part, Zaragoza is relatively undiscovered as far as major Spanish cities go.

Thank you Carlos. Your advice is fantastic and we will look into this.

We really enjoyed our 3 days in Zaragoza last Summer. For us, it was the stop between Irunea and Barcelona.
Here are my must dos:
1. EMOZ - http://www.emoz.es . An amazing origami museum. https://www.tripadvisor.com/Attraction_Review-g187448-d7140299-Reviews-Emoz-Zaragoza_Province_of_Zaragoza_Aragon.html
2. A meal at Meli del Tubo. https://www.tripadvisor.com/Restaurant_Review-g187448-d10678336-Reviews-Meli_del_Tubo-Zaragoza_Province_of_Zaragoza_Aragon.html . We had a 2+ hour lunch. I still dream about the Cave Ovum.
3. https://en.wikipedia.org/wiki/Aljafer%C3%ADa

Take a taxi from/to the train station as it is not near the city center.

P.S. There is a Taco Bell on one of the main tourist streets. https://www.tripadvisor.com/Restaurant_Review-g187448-d10108577-Reviews-Taco_Bell-Zaragoza_Province_of_Zaragoza_Aragon.html

Taco Bell, really! With all the good Spanish cuisine, there should a law against eating at Taco Bell in Spain. Joking aside, in addition to Zaragoza, there is the smaller town of Siguenza or Alcala de Henares, where you could easily spend a few hours.

If you train in to Zaragoza in the morning, I would recommend your first stop be at the Aljafería Moorish Palace which opens at 10:00 am. Admission is only €5 and they also have Spanish, French, and English guided tours too, which are very well done, the tours even show the Regional Parliament of Aragon (which is also located in the Aljafería Palace). To see all the Palace takes about 2 hrs.

From the Aljafería, make your way to Basílica de Nuestra Señora del Pilar, which is a huge church in the old center of the city. The Basílica is a major pilgrimage site of the Virgin Mary of Pilar, you can tour it on your own (no tickets necessary).

In front of the Basílica is a huge plaza that has parts of the old Roman walls of Zaragoza as well as the subterranean Roman Forum museum.

I would then go for lunch at the close by Mercado Gastronómico on Calle Mártires, which is a market with various gourmet food stalls, with very responsibly priced goodies from across Spain. Here is their website: http://www.puertacinegiagastronomica.es/

If you have any more time left before your train to Madrid, I would walk to the nearby Roman Theater of Caesaraugusta, one of the largest Roman Theaters in Spain, they have a good museum there too that explains about the history of the Roman Theater and its discovery.

Hope this helps :)

Thank you again for all your advise.