First of all, I would have to say that you live in a beautiful part of the US! I used to live in Fort Collins, and drove up in your area quite a few times. Great hiking country!
For the trip to Peniche (I have never been there), I think I would recommend the bus. Buses in Spain are usually a better way to travel that trains. Usually buses are more comfortable and faster.
Have a look at http://www.alsa.es (Click "English" in top right corner for a better understanding). They have a bus to Lisboa from Santiago de Compostela... its itinerary says it has the following stops:
these are aproxímate times.
City Arrives Leaves Days
SANTIAGO COMPOSTELA 10:00
PONTEVEDRA 10:45 10:45
VIGO 11:15 11:15
VIGO Aeropuerto Peinador 11:30 11:30
BRAGA 11:45 11:45
OPORTO Aeropuerto Sa Carneiro 12:30 12:30
OPORTO 12:45 12:45
ALBERGARIA 14:15 14:15
COIMBRA 15:00 15:00
LEIRIA 16:00 16:00
FATIMA 16:30 16:30
LISBOA ORIENTE 18:00
... once you are in the general area you would need to change to local transportation to get to Peniche. Not sure about what would be the best way, but the Alsa bus might stop at the bustation in Leira or Fatima and then you could maybe get a local bus from there?