You can visit Spanish an French Railways companies at http://www.renfe.es and http://www.sncf.fr respectively. So you can do a better idea of how much time you need and if it is too much or not comparing to the plain.

Travelling by train gives you an oportunity to stop and visit the places you find during the trip, the plain not. The plane is faster, much faster, so if you plan not to stop in any place in the road is better the plane.

>From Bilbao to Pisa you have, more or less the following posibilities: Bilbao-San Sebastian-Zaragoza-Barcelona-Marselle-Nice-Monaco-Firenze-Pisa.

Regards,

Aitor