If you haven't booked the trains yet, it will likely be cheaper to fly. I just got back from Spain and took the train from Barcelona to Madrid, and you ideally should book as soon as possible in order to get the best deals. In terms of the "availability," the trains run at least every hour during the day, and are generally very punctual.

I second the previous suggestions that you should try to avoid the touristy areas in Barcelona (and even Madrid) for meals. It'll be hard, but I found the food to be better.

If possible, I definitely recommend strolling through the Gothic Quarter in Barcelona. There are so many hidden bits of history that you may stumble across.

Have fun on your trip! I already miss those cities -- except traffic in Lisbon