Once I have finished the Basque Country tour, what is the best way to get to Barcelona, maximum of two days between tours.
Low cost flight: http://www.vueling.com/en alternatively train (much slower): http://www.renfe.com/
Yep go with Vueling
There are only two direct trains per day, departing Bilbao about 6:30 a.m. or 3:20 p.m. and taking 7 hours to Barcelona. Departures with one connection take longer, and cost more if the connection is in Madrid. Flying can be quite affordable, as well as faster.