Quick answer
Which churches should you include in a Porto route?
Start with the Sé Cathedral, Clérigos, Carmo, Santo Ildefonso, Capela das Almas and São Francisco if you want the most iconic churches. Then add Bonfim, Lapa, Misericórdia, São Nicolau, Trindade and smaller chapels if you want a more personal and less obvious route.
For a goldenporto-style route, do not rush. Look at the façades, tiles, towers, bells, street angles, interiors, views and the way each church changes the mood of the surrounding neighbourhood.