I haven't gotten to Bordeaux or Bayonne; they're on my list for a trip to western France in 2019 or 2020. I see that connecting Toulouse to San Sebastian by train is not an easy task, requiring you to pass through either Narbonne and Zaragoza or Bordeaux. Not a problem if you have time to see those cities. Otherwise, ALSA, Ouibus and Flixbus all have much faster service. You may already have discovered this, or perhaps it was discussed in your earlier thread.
Just before you reach SS (no matter what path you take) you'll pass through or near Hondarribia, which is definitely worth a visit. I don't know that there's a place to store luggage, however, so it probably makes more sense to visit it on a day-trip from San Sebastian.
As for San Sebastian and Bilbao: For me, there's more to see in Bilbao and I found the intense level of tourism in the smaller SS historic district somewhat off-putting, but there are more coastal side-trips from San Sebastian. You can get to the very interesting interior capital of Vitoria-Gasteiz from either Bilbao or San Sebastian.
In addition to consulting your guide book, I suggest looking at Trip Advisor's Things To Do lists for the two cities to see what specific attractions (museums, etc.) interest you. Add time for just wandering around (about half a day in SS, more if you want to walk all the way around the large beach; closer to a full day for Bilbao due to the larger historic district and the river-side walk). Then consider how many day-trips you'd want to make from each place.
If you have extra time, the Euskotren between Bilbao and SS takes a pretty route and affords an opportunity to see a rural part of the Basque Country. The trip takes about 2 hr. 45 min., and there seem to be departures every hour. I've linked to the current schedule; there may be some tweaks in June. The train has a sort of subway-car feel, with plastic seats.
