That sounds like a very tight schedule!
It seems you can't get an e-ticket on the voyage-sncf website for a ticket to SJPdP: when I try it, it only shows a buy-online/print-it-at-the-station option. Which is not helpful in your case...
I don't know Biarritz's station, but I wouldn't believe it's big.
I know for sure Bayonne's is not: it's easy to find your way. There are monitors in the entrance hall (huge one above your head, small ones when going to the platforms) and on the platforms. Note that for the small ones, blue is for departures, green for arrivals. Stairs and tunnels to access the different platforms.
Like
@whariwharangi pointed, there is a train from Biarritz to Bayonne leaving at 1745. If you manage to get to Biarritz's station on time, you can buy an ticket from Biarritz to SJPdP at once. There will be a change of trains in Bayonne and 10min to do it.
Whatever your choice, you can buy your ticket from a person at a counter or from a TER machine (blue ones, I think there are also in English. Yellow ones are not the ones you want, they're for inter-national tickets). First option can be trouble if the person doesn't speak English; second one too because it's a machine (always a bit stressful whenone is not used to it...)
Like said before, why not take your time? Bayonne and SJPdP are nice places to visit
Bayonne tomorrow night and SJPdP on Thursday, smooth departure on friday
In case, here are some addresses for pilgrim's accommodations in Bayonne (because on one of the French Caminos) (don't know if they're updated!):
http://www.xacobeo.fr/ZE1.11.Aqu.Lit_PA_heb.htm