Check the link that Annika gave you for the Bernina Express.
It has sections.
www.myswissalps.com/be rninaexpress/gettingth ere
And/or, use the timetable link that Annika gave you, with the cities that are included, which you can see on a map:
The full route goes from Tirano to Chur
if you are going to do all that you have suggested in 6 days or so, you need to learn to use the timetable and maps. And, you'll be doing a lot of riding on trains.
Late September can be very nice near the Jungfrau. Attached pictures were taken in the last week of September in 2009, at Männlichen or near it..
Once you have made a guess at an itinerary, post it, and we'll comment - politely of course...;-)
Re - Paris and Frankfurt -
Please leave your jet-lag in Frankfurt.
Leave for Paris from Zürich or Basel, I think. Maybe Bern. Arno and Annika can suggest the best route, but those could all work well.
Frankfurt to/from Basel or other major Swiss cities is a pretty straightforward option, but, of course that would skip Paris.