I suppose you will travel in July/August, otherwise boat rides wouldn't make much sense.
Geneva, Lausanne, Montreux are just 30 resp 20 minutes by train from each other; may be it would be easier to choose just 1 place for your stay in the Lake Geneva area.
You can go by boat from Geneva up to Lausanne and Montreux:
Geneva dp 10.15 - Lausanne 13.50/14.15 - Montreux 15.40 - Chillon castle ar 15.50
Geneva dp 12.20 - Hermance 13.05/13.10 - Nyon 13.40/13.45 - Yvoire 14.05/15.12 - Thonon 16.00/16.10 - Lausanne ar 16.50
Geneva dp 14.50 - Lausanne 18.25/18.40 - Montreux ar 19.25
The Rochers de Naye railway is NOT included in the Swiss Pass. You will have to pay half fare from Haut ce Caux up to the top and back (CHF 12.50/pax).
Montreux - Gruyeres - Murten/Fribourg:
May be you will need the whole day for the Gruyeres area. Left luggage at Bulle railway station. Train from Bulle to Broc Fabrique where you may visit the Cailler chocolate factory: http://www.cailler.ch/en/Chocolaterie/Information.aspx
From Broc you can walk (hiking trail) to the medieval town and castle of Gruyeres or you can take a bus from Broc Village (dp 11.05, 12.05, 12.57, not daily, have a look at the timetable) up to Epagny Village, just below the castle and go up to the city gate on foot. Or take the train via Bulle. Castle in the old town, cheese diary at the Gruyeres railway station.
The whole area can also be visited in a day trip from Montreux (chocolate train): http://www.goldenpass.ch/CMS/default.asp?ID=414
Murten can also be reached by boat, from either Yverdon (20 min by train from Lausanne) or Biel/Bienne (25 min by train from Bern):
Yverdon dp 10.50 - Murten ar 15.50, change boat at Neuchatel
Biel/Bienne dp 9.45 and 14.40 - Murten ar 13.00 and 18.30
Just 1 full day for Bern is fine, unless you spend hours and hours in museums.
Thun (less than 20 min by train from Bern, 4 trains every hour) can be visited in a few hours. The boat ride over the lake is fine. You may stop over at Oberhofen castle (museum) and Beatus caves.
There is absolutely nothng to see at Interlaken but tourists from overseas: just 2 railway stations and 2 boat stations, many hotels and souvenir shops, 2 supermarkets and some restaurants; the best you can do there is to change from one train/boat/bus to another.
Neither Lauterbrunnen nor Gimmelwald are real gems, although they are very popular with people from overseas. Wengen would be the better choice.
The Jungfrau railway is very expensive and they give only 25 per cent discount to Swiss Pass holders. A return ticket from Wengen will cost 117 CHF (with Swiss Pass). Up to Jungfraujoch and back to Kleine Scheidegg costs 100 CHF.
BTW: a ticket from Zermatt to Gornergrat and back costs 39 CHF with the Swiss Pass and the panorama from there to uncountable glaciers is as breathtaking as from Jungfraujoch.
There are different trails from Kleine Scheidegg to Wengen, all nice and well signmarked. Kleine Scheidegg - Grindelwald is feasible too, the trails are good, but it's much longer.
Kleine Scheidegg - Murren would be a strenous full day hike: you must first go down from Kleine Scheidegg (2160m) to Trummelbach (810m), then along the Lutschine to Stechelberg and finally to Gimmelwald and Murren (1640m).
In my eyes, Zermatt and surroundings are more attractive than the Jungfrau area. I would stay less days in the Bernese Oberland and spend much more time around Zermatt and St. Moritz. 2 nights are just not enough for these places.
There is absolutely no need to take the Bernina Express. The local trains offer fine views too. The reservation fee for the Tirano - Lugano bus is 12 CHF. As an alternative, you could take a Italian train up to Lake Como (every 2 hours). An ordinary train ticket from Tirano to Bellano costs EUR 6.25/CHF 7.60 and a boat ticket from there up to Como EUR 9.30/CHF 11.30. The Como citybus goes from there to the Swiss railway station of Chiasso.
So your trip could look like this:
St. Moritz dp 9.45 - Tirano ar 12.21, dp 13.10 by train to Bellano ar 14.32, dp by Lake Como boat 15.16 - Como ar 18.00.
It would also be possible to leave St. Moritz at 7.45 by train to Bernina - Tirano - Varenna, to cross the lake by ferry and to go on by bus from Menaggio to Porlezza, where you could board the 16.30 hours Lake Lugano boat (included in Swiss Pass) and ride up to Lugano.
Bellinzona is a nice small town, but Lugano and Locarno are more attracive. As the trains between these 3 places run at least every 30 minutes, you don't need to sleep at Bellinzona. There are hand luggage lockers at the railway station.
some links:
Have a look at http://www.myswitzerland.com/en/home.html and the many links you will find there
http://www.rhb.ch/Video-Glacier-eng.784.0.html?&L=4
http://www.rhb.ch/Video-Bernina-eng.782.0.html?&L=4
http://www.rhb.ch/UNESCO-Clip-eng.1061.0.html?&L=4
http://ballenberg.ch/en/Welcome
http://www.cgn.ch/horaires/pdf/AffA2-ete-10.pdf
http://www.cgn.ch/eng/flotte
http://www.blonay-chamby.ch/index-en.php
http://www.chillon.ch/en/
http://www.chateau-gruyeres.ch/e/multimedia/spectacle.html
http://www.la-gruyere.ch/en/navpage-ExcursionsFR-HistSitesFR-120085.html
http://www.lamaisondugruyere.ch/index.php?option=com_content&view=article&id=142&Itemid=56
http://www.lamaisondugruyere.ch/index.php?option=com_content&view=article&id=142&Itemid=56
http://www.chatelard.net/english/pages/descr_e.html
http://en.wikipedia.org/wiki/Emosson
http://www.emosson.ch/PublicEN/default-en.htm
http://www.gornergrat.ch/home/index.php
http://www.klein-matterhorn.ch/photos/
http://www.zermatt.ch/en/index.cfm
http://www.murtentourismus.ch/en/navpage-DestinationsFR-MurtenFR-99305.html
http://www.murtentourismus.ch/en/welcome.cfm?
http://www.avenches.ch/en/page.cfm/siteetmuseeromain
http://www.maggiore.ch/?lang=en
http://www.illagomaggiore.com/?set_language=en&cl=en
http://www.lagomaggioreturismo.it/ing_home.html
http://www.lagomaggiore.net/uk/
http://www.lagomaggioreonline.com/?newlingua=UK&
http://www.ascona-locarno.com/