I have two days 13th and 14th of October to travel by train staying overnight somewhere along the way and getting off here and there to explore villages, scenery, a chairlift etc. Does the train go out and then come back on the other side of the river? There are so many villages along the way I’m not sure which would be a good selection to stop and explore. Also any suggestions where stop for an overnight hotel before a train back to Frankfurt? Should I book train tickets now or can I book on the day?
I would go to Rüdesheim early on 13th by train from Frankfurt 1hr 20 min
See bahn.de for direct train connections
Check in Hotel early and do a boattrip(roundtrip) after lunch on the Rhine
from Rüdesheim to St Goar(Loreley) and back See website
You will return past 7pm to your Hotel (check tripadvisor for reviews)
and there is a nice Inn in the vineyards above town (see link) but you ll need a taxi from train station to get there
Next day 14th see Rüdesheim and do the chairlift to Niederwald Monument above town and river
Return to Frankfurt in the evening by train
Rüdesheim takes about 45 min. to see. If you like, arrive, walk around town, take the ship to St. Goarshausen, take the train back to Rüdesheim. Ride the gondola up to catch the sunset. Finish your evening at Rhein Wein Welt which is directly across from the train station.
Next day, take the ferry from Rüdesheim, across to Bingen. Ride the train up the left side of the river, and get off in Bacharach, Ober-Wesel and St. Goar. Go explore Burg Rheinfels. Take the ferry across to St. Goarshausen and ride the train back to Rüdesheim.
Alternative is to stay in Eltville and do the short train ride to Rüdesheim to do the other stuff. Eltville is not as touristy as Rüdesheim and has a lovely promenade walk along the Rhein, without trains going past. When you come back after your ship ride, your train will also stop in Eltville as it is only about a 10 min. ride past Rüdesheim.
"There are so many villages along the way I’m not sure which would be a good selection to stop and explore."
For leisurely village-exploring, I suggest targeting Bacharach and Braubach for at least a couple of hours each.
Bacharach: https://www.mittelrheinentdecken.de/en/villages-towns-and-cities/bacharach/
Braubach: https://www.wohnmobilstellplatz-braubach.de/1325-jahre-braubach/braubach-in-bildern.html
Boppard is my recommendation for an overnight stop. Here you will have proximity to a wide choice of hotels and restaurants, some right on the riverfront, to the Rhine's best (IMHO) chairlift ride and river views, and of course good transportation.
https://www.youtube.com/watch?v=x1s0ReHNdLQ
The trick is putting together a travel plan. This is how I'd do it. You'll be on a schedule, but the walks are not very demanding, and much of the time will be sightseeing from a boat, a train window, or a chairlift ride.
Oct. 13: Boppard, Braubach
You can get to Boppard by direct regional express train (9:08 - 10:39, for example.) The station is close in, so it should be a short walk to most hotels. Drop bags there. Take a walk around town.
12:12 - 13:05: train ride to Braubach, tour town on foot. Return 15:53 - 16:44 by train, or stay for dinner and return later. Zum Goldenen Schlüssel is a good bet for German food if you stay.
Oct 14: Rhine cruise, Bacharach, Chairlift
Chairlift is open 10:00 - 17:00. Nice views from Gedeonseck, a nice spot for a meal and a short walk from the top:
https://s3-media1.fl.yelpcdn.com/bphoto/T9oxNMwLvt_-r5nCsce-jg/o.jpg
But first... rise early, check out, drop bags at front desk catch a train to Bingen Rhein Stadt station (7:44 - 8:28.) Then board the day's first cruise boat (9:15 - 10:00 with K-D) to Bacharach for a 2-hr. walk around town. Then complete your cruise to St Goar 12:00 - 13:15.
Train back to Boppard takes 12 minutes (14:00 - 14:12.) If the weather is good, do the chairlift after that.
Return to Frankfurt 17:16 - 18:47 or 19:16 - 20:47 by direct regional express train.
There's also an earlier 15:16 - 16:47 train to Frankfurt if you don't do the chairlift.
Train rides are largely free after arriving in Boppard (VRM Guest Ticket.) Any tickets you need to buy can be had on the day of travel, no advance-purchases are needed.
While Burg Rheinfels castle ruins , currently closed AFAIK, is worth visiting, I did not suggest it on the grounds that construction schdeuled into 2028 may in fact mess with your visit... per the website:
"Ziel ist es, die Sanierung der Burg Rheinfels bis 2028 abzuschließen..."
Also, St Goar itself is less interesting than the other towns and would mean an additional stop for which time is not all that available.