We are signed up for Basque Country ending on Sept 6 (so basically have that day free) and then start the Portugal Tour in Lisbon on the afternoon of September 10. Any suggestions as to how we might best spend the time in between. Would like to know about cities to visit, sights to see and best transportation between northwest Spain and Lisbon. Thanks!
There are very few trains between Spain and Lisbon. See info at https://www.ricksteves.com/travel-tips/transportation/trains/spain-rail-passes (more detailed map coming soon), including links for the national railway network and two coastal railways. There's an overnight train departing from the France/Spain border that serves these boarding points:
San Sebastian
arr 19:08
dep 19:10Vitoria/Gasteiz
arr 20:45
dep 20:46Miranda de Ebro
arr 21:07
dep 21:08Burgos Rosa de Lima
arr 21:58
dep 22:00Valladolid Campo Grande
arr 23:08
dep 23:10Medina del Campo
arr 23:51
dep 00:11Salamanca
arr 00:57
dep 01:00
Burgos would be a logical town to visit, with an old town and gothic cathedral, served by train from Bilbao (the end of your tour), and along the route of the night train. From Burgos to Leon is another easy train route. From either Bilbao or Leon, you'd still need to connect to the night train at Miranda de Ebro or Medina del Campo.
If you travel further west in Spain, such as from Bilbao to Santiago de Compostela (minimum 10 hours by train), then your most convenient connection toward Spain may start with a bus between Santiago and Porto. The train connections there are in daytime but are not terribly convenient.
You can also fly from Bilbao airport; see https://en.wikipedia.org/wiki/Bilbao_Airport and www.skyscanner.com.
You may also enjoy driving, which is most flexible, but should drop the car within Spain to avoid a high drop-off fee in Portugal.