Switzerland, need ideas for two nights!

The reason you can't find any of the named scenic trains on the south side of the Bodensee is that you will be in the (relatively) flat lands of Switzerland and the named trains tend to stay in the mountains. The south side of the Bodensee is much like Wisconsin. But you don't need a named train to get you from where you are to where you want to go. Are you buying some sort of Swiss rail pass or buying the tickets as you go? The most direct route is from Rorschach or Rorschach Hafen (harbour) towards Romanshorn which is the main rail hub on that side of the Bodensee. There is a regular S-Bahn (S8) leaving at 7 past the hour from Rorschach and one minute later from R. Hafen (don't know which is closer to your arrival)for which the calls are: Rorschach Rorschach Hafen Horn(Bodensee) Steinach(Bodensee) - this is a lovely old town, one of the best Arbon Arbon Seemoosriet Egnach
and Romanshorn about 20 minutes later. The train will be marked S8 and probably Schaffhausen. ... more

... continued You have 14 minutes to catch the train to (probably) Brig via Amriswil Weinfelden Frauenfeld Winterthur Zürich Flughafen (airport) Zürich HB and Bern where you only have 6 minutes to cross the platform to the train to Interlaken Ost. Sometimes those are Swiss trains, sometimes they are German ICE or French TGVs. None require reservations so you can use them all equally.
You will arrive at Interlaken Ost about 3:49 after you left Rorschach. You could build in a more scenic ride, although the bit from Bern to Interlaken is pretty darn good by changing in Zurich and again in Luzern onto the narrow gauge ZentralBahn rack railway over the Brunig Pass but that would add extra hours and you can do that one going to Luzern. From Interlaken Ost to Muerren is the time honoured way outlined in the RS Guide.

You could easily fit in the train portion of the Bernina Express. Rorschach to Chur is only 1 hour 10 minutes: Rorschach to Pontresina is 3 hour 35 minutes. If I were doing this, I would look at going from Rorschach to Pontresina on the first day (Oct. 2); take the regional train over to Tirano and back to Chur the second day (Oct. 3), and than go from there to Mürren on Oct. 4. The trip from Chur to Lauterbrunnen is just under 4 hours, and from there you just hop on the cablecar and ride another short train to Mürren. (Nigel might recommend staying in Samedan instead of Pontresina, and if so, listen to his advice, as he has been there and I have not).
And if my plane from Zurich were departing in the afternoon instead of the monrning, I would consider rearranging the order of things, moving Luzern up and saving Mürren for last. Then it would be 2 nights Pontresina, 2 nights Luzern, 3 nights Mürren, and head to the airport from there.

I most certainly would recomend staying in Samedan if I knew where to stay. It is lovely countryside and I have spent several hours there. But never overnight. We stayed in Chur.

I used to live in the Engadin and Samedan isn't that beautiful as some of the villages a few minutes by train away. Personally I'd recommend Zuoz, Guarda or Ardez as spots to overnight. Zuoz is only about 15 mins from Samedan and is for the most part a beautiful very traditional Engadin town. Guarda is much like a Tuscan hill town in that its perched on a hill and absolutely gorgeous but a little further away. Either way I highly recommend taking a train from Chur to Samedan and then the next day another train over the Bernina to Tirano. Both are UNESCO world heritage sites and the scenery from the train is amazing. BTW: You dont need to take any of the Express trains, eg Bernina Express, as a local train is as fast, travels the same route and is filled with locals rather than tourists. Finally, on the Chur to Samedan leg make sure that your train travels the old line via Filisur not via the new Vereina tunnel. See www.sbb.ch for train schedules to help you plan all this. PM me if you'd like recs on the Berner Oberland or Luzern.

I'm a big fan of Pontresina - especially if you want to do some hiking. We stayed at Hotel Engidinerhof last fall. They provided a rail pass for the region which we took advantage of for day trips and also for hiking to a destination and making the return trip by train.