itinerary help: 10 days and many hiking trails

This day 2: Wengen (3h train from Zurich)
Hike from Wengen to the Kleine Scheidegg (7km / 3h)
Hike from Kleine Scheidegg to Männlichen (4.4km / 1h30), cable car in Männlichen to Wengen seems like a very long day. I would set my hiking expectations to a little less ambition on a travel day, but you might be able to do it if the weather cooperates. I would save the Schilthorn for a morning start as the weather is often best then, so maybe you do the Schilthorn on Day 3.

Be sure to make reservations for the Large Hadron Collider at CERN. We did but there were lots of people showing up without and being turned away.
You aren't early enough to get reservations to actually go down and see the collider (those are gone within minutes of being posted a year in advance) but you can probably still get a spot for the tour of the main building, control room, and museum. The tour guides are the scientists who run the collider...I learned more in the 3 hour tour than I ever learned in any of my science classes at university!

Wengen to Kleine Scheidegg is really only two hours so it is quite possible to do that and the Männlichen trail plus cablecar down to Wengen in an afternoon.

By Eiger Trail do you mean the Eiger Northface Trail? Do you want to hike it up or down? A nice way to do this from Wengen is to take the train up,to Kleine Scheidegg and then onward with the Jungfrau railway to the trailhead at Eigergletscher. Hike down to Alpiglen where you can catch the train down to Grindelwald to explore.

For the Trift bridge hike, you would train to Meringen, then Postbus to the Triftbahn cablecar. I do not how long that travel will take but SBB.ch will tell you. The hike is relatively short so not problem fitting this into a day.

St. Moritz and Zermatt: do you really want to do two long train rides ( full days) to do one hike in each place? There are so many great hikes from each location. What if the weather is really bad on the appointed day? You have ridden a train all day and spent an expensive night in a place only to get rained out. I would suggest you pick one or the other and spend four nights to get the most out of your hiking time.

Laurel and Lola:
My plan for day 2 is if for some reason I cannot do the hike to Männlichen, I'll go back by train or walk the reverse route to Wengen, would that work?

Anita:
Thanks for the tip, I'll make the reservation as soon as I finish this itinerary.

Lola:
By Eiger trail I mean http://www.myswitzerland.com/en-ca/eiger-trail-the-swiss-alpine-experience-trail.html. The plan for this day is: 1h train, 2h hike, around 2h exploring Grindelwald, 1h train back.
I really want to see the Trift Bridge, that would be the first thing in the day and after that if I still have time, I would visit Jungfraujoch or Schilthorn.
About St. Moritz and Zermatt, good point, I think I'll skip St. Moritz, I noticed that the CERN tour requires 3h so I added one more day in Geneva. Now it would be:

• day 5: Zermatt (3h train from Wengen)
  explore Zermatt

• day 6: Zermatt
  Hike Matterhorn Trail (10km / 3h)
  If still have time, one short hike

• day 7: Zermatt
  Mountain bike trail

• day 8: Geneva (4h train from Zermatt)
  UN

• day 9: Geneva
  Large Hadron Collider (at CERN, 30 min bus from Geneva)

Thoughts?

I'm about to throw a giant monkey wrench into your carefully planned itinerary. What if you run into bad weather (which you will at some point)? You haven't given yourself any flexibility. If either of the full days you have allotted for Zermatt and St. Moritz are rainy, these excursions will be a waste.

General rule in the Alps- without the benefit of a short-term weather forecast, spend at least three nights at any location. This gives you more of a buffer in case the clouds roll in one day. For the same reason, don't try to pigeon-hole particular hikes to a certain day in advanced. Let the conditions dictate your daily activities, prioritize which hikes you most want to do, and jump at the first opportunity the Alpine weather gods afford you.

EDIT: Oops, I see you already made adjustments...