Two of my favorite meals in Spain were at
Paco Meralgo in Barcelona and
Triciclio in Madrid.
The
Time Out food hall in the Mercado da Ribeira at Cais do Sodre in Lisbon has some of the best food options in town served by several of the highest profile chefs in the city. You've got to try the pastel de nata at
Manteigaria. They are in Bairro Alto, but also have a place at the Mercado da Ribeira.
In my opinion, Madrid deserves a longer stay than Lisbon.