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1) Lots of options to do what you want. You can best check out these planning guidelines to make a plan that exactly fits your interests. For the Jungfraujoch trip you'd best be based in Interlaken or one of the villages south of that, like Grindelwald, Wengen or Lauterbrunnen. See the links for activities, bad weather alternatives, hotel suggestions, etc. Your first stop could be Lucerne, where there is a lot to see as well, and your second stop the Interlaken area, the be reached via the Golden Pass line.
2) Only a few people suffer from that. I don't know if you're one of them. Just take it easy, walk slowly, sit down regularly, and go down if you don't feel well. Don't take young children up to that altitude, see the Jungfraujoch page.
3) Simply fill out your trip in the timetable to check your options. The best pass depends on your plans. Once you have a plan, you can pick the one that fits your needs. Most people pick a Swiss Travel Pass or a Swiss Half Fare Card. If you want to be sure to pick the cheapest option, you can do some calculations as explained here.
Does this get you started?
Appreciated. We have started our hotel booking at Zurich and Wilderswil as a base. The accommodation (a studio apartment) that we booked via booking.com has a very reasonable price but it has a non-refundable deposit of one night. We found interesting rule on how to pay the deposit afterward. Booking.com did not charge us. The owner of the place will send us instruction on the wire transfer the $ to them directly. We wish to know how we can check the credential of this place. We worry about that it will be too late to find another backup accommodation when we have arrived Wilderswil and found out the accommodation is not available or closed down.
Will the 3 day Flexipass work for the following itinerary? I assume that the Swiss Pass will not include City night line to Prague. I put my questions in "bold".
Day 1: Flight arrived Zurich in the evening, night stay Zurich
Day 2: Zurich day tour, night stay Zurich
Day3: 1st day Flexipass- Zurich to Rhine Fall . "The Rhine Falls are within easy reach from Zurich (an hour by train), and not to be missed. This day trip takes about half a day. You can extend it by exploring the town of Schaffhausen or do a two hours boat cruise to Stein am Rhein and take the train back to Zurich from there. This detour would add another 4 hours to your trip" Return to Zurich to pick up luggage, train to Wilderswil via Golden Pass Line (should we visit Lucerne first and go to Rhine Fall before we head to Basel on Day 7?); night stay Wilderswil
Day 4: Early morning train and use Flexipass discount to go Jungfraujoch (can we use both discount?), night stay Wilderswil
Day 5: (from this website)" explore the valley on foot. This hike can be as long or as short as you want. You can start in Wilderswil (5 minutes from Interlaken by train), and walk via Zweilütschinen and Lauterbrunnen to Stechelberg and beyond. The trails are not difficult. Trains back to Interlaken depart from Zweilütschinen and Lauterbrunnen. From Stechelberg there's a bus back to Lauterbrunnen. The highlight of the route is the Staubbach Fall, just past the village of Lauterbrunnen." , night stay Wilderswil
Day 6: 2nd day Flexipass- Please advise where to go, night stay Lucerne
(Day 4,5,6 can be interchanged depending on the weather to go Jungfrau)
Day 7: 3rd day Flexipass- sightseeing Lucerne, "travel by train to Arth-Goldau, and switch to the cogwheel train up the Rigi. From there, another train goes down to Vitznau. Optionally you can walk part of this route to explore the car free countryside even better. The section from Rigi Staffel to Rigi Kaltbad is a short and easy hike. Vitznau is a beautifully located village long Lake Lucerne. A relaxed boat tripis the perfect way to reach Lucerne again to pick up luggage. Then to Basel before 9 p.m, night train to Prague . (Will this work?)
Looking forward to your reply.