I traveled through that area in the same direction during 2017. There are many great places to stop, and the more places you stop the likelier you are to be on fixed-price regional trains (TERs) or buses rather than the costly-at-the-last-minute TGVs. I just bought tickets on the day of travel or the day before. You can take a look at fares on the SNCF website.
In the area around Perpignan (I'm not sure of the geographical extent) I encountered 1-euro fares for some trips on both trains and buses. I think there were some brochures floating around; keep your eyes peeled in train station in that area. You can also ask at any tourist office you encounter.
A trip I especially recommend is the Yellow Train through the Pyrenees that runs between Villefranche-de-Conflent Vernet les Bains (wildly picturesque but also wildly touristy) and Latour de Carol. Regular trains run from Perpignan to Villefranche. I believe you could make a round-trip on a single day. The best scenery is in the middle of the trip, so you wouldn't have to go quite all the way to Latour de Carol before turning around. I believe the schedule shows more frequent trains on the middle section of the narrow-gauge line. I'm not sure of the frequency during October, though.
For what it's worth, these are the places I stopped either overnight or on daytrips: Montpellier, Sete, Narbonne, Pezenas (craft town), Perpignan, Collioure, Banyuls, and Ceret. Montpellier, Narbonne and Perpignan are good-size places; the others are rather small, and you could probably take in all their sights within a few hours.
On the Spanish side of the border the obvious places to stop are Figueras (if you're interested in seeing the Dali Theatre-Museum, for which you'd want to buy your ticket ahead of time) and Girona, which has a walled medieval district. The bus trip from Figueres to the coastal village (now touristy) of Cadaques is very pretty, and Cadaques itself is lovely.