Woops...this is now too late but in case anyone else looks at this post in the future. My bf and I went to Chile a while ago and also took a side trip from Santiago to Valparaiso. We ate at Pasta y Vino in Valparaiso and thought it was excellent -- great pasta with fresh ingredients -- so I definitely recommend this place. I think people generally reserve in advance but since we're Americans, we were there right when they opened for dinner (9pm!) and got last-minute seating at the bar and got to watch the action in the kitchen.
Hope its not too late but DEFINITELY go to the upstairs of the farmers market (old yellow and iron building designed by Eiffel) and eat at one of the seafood places. Its as much Valpo character as you can find. The best one is Rincon del mar I believe. It will be packed out the door everyday of the week.