Planning to travel through Portugal for 2 weeks beginning the last week of May. I would like to spend a 3rd week traveling to Barcelona and perhaps San Sebastian. Would appreciate any suggestions on getting there and places to stay. Thanks!
Trains are sparse between Portugal and Spain. You can take an overnight train from either Lisbon or Coimbra to either Madrid or San Sebastian; there are no daytime trains on either route. From San Sebastian to Barcelona, there are a couple of direct, daytime trains each day that take 6 hours. How to Look Up Train Schedules and Routes Online gives you the DB train schedule link and tips for using it. Train tickets can be cheaper in advance, if you're ready to lock in dates and times, but they are also sold at train stations and some travel agencies over there.
To compare budget flights, see www.skyscanner.com. Car rental is not necessary to connect these cities and there's a large fee if you pick up and drop off in different countries.
We traveled by bus from Coimbra to Salamanca in May 2012. We purchased the tickets while in the US and saved about 40%. Let me know if you would like more information.