I haven't found any schedules either, but perhaps you need to aim for Lyon in France, and transfer to Le Puy from there. You might find the easiest way to get to Lyon would be to get the bus from Girona airport to either Girona or Barcelona, and catch a train from there. http://en.wikipedia.org/wiki/Girona-Costa_Brava_Airport
I found this bloghttp://on-a-train.blogspot.com/2008/06/barcelona-to-girona-to-cerbere-to.html These people travelled from Girona to Lyon, via Cerbere to Montpellier, then via TGV to Lyon.
Is your Girona ticket fixed already? There would be closer airports in France to get to Le Puy from: it will probably cost quite a lot in train fares to get from Girona to Le Puy, and will possibly need an overnight stop somewhere with all the transfers.
Hi, if you check out http://www.reiseauskunft.bahn.de you will get all the connections from Girona to Le Puy. I checked the timetable for 8.1.2009, if you check too far in advance you may not get any info, because the timetable is only valid up to a certain date. According to the info I got the travel time is around 20 to 22 hours with a few changes. You want Le Puy en Velay Faycell by the way, the Hermitage station is out of town. Good luck, Gitti