Undecided on Swiss Pass purchase

You've done your homework! I'll look this over and get back to you.
Couple of points: Swiss Pass covers virtually all local transportation as well as many museum entry fees.
I saw something just today that I would like to confirm. I no longer see the note 2 on the Swiss Pass synoptic map that says you only get a 25% discount on the Jungfraujochbahn. So I want to research a bit as maybe it has changed and you get the normal 50% as the rest of the mountain railways marked by dotted lines. But with a pass as it was, it would cost 135 out of pocket with the Swiss Pass, but with the pass its is free to Wengen, so it is less.
Your calculations show $ and should be chf. They're close, but chf are still a bit more than $

And the answer is (drum roll) The One Month Half Fare Card
Nobody ever wants to hear this, but it saves the most money. You still have to buy a ticket every time you travel, you just pay half price. It includes local transport but no museum fees.
I figured your total travel from landing at Zurich airport to arriving at Domodossolo, Italy on the way to Stresa.
I come up with full fare cost of 463 chf. Half fare is 231.50 chf plus 120 chf for the card gives 351.50 chf.
The next least expensive is the 3 day Flexi Pass with the days used as 2, 4, and 6. That comes to 424 chf.
I checked four other scenarios, and nothing comes close to the half fare card.

What you cannot calculate into the price is the "convenience" factor of the Swiss Pass. Jumping on and off as many times as you like wherever and whenever really cannot be priced out.

In your calculation of prices you included the rail prices but only 25% of Jungfrau. If you don't have a pass you have to pay 100% so that number is incorrect to do a comparison of with pass and without pass.

@ Tim - That is very true, but you can still hop on and off in a day, to a certain extent. The OP is landing at Zurich airport, then going into Zurich for a few hours to explore before continuing on to Luzern. They could buy a single ticket from the airport to Luzern, get off at Zurich Hbf, tour around the city, then when they want, hop back on the train and proceed to Luzern. As long as they don't deviate from the original itinerary, they're OK.
On the other hand, with a pass, you could also use the trams in Zurich without buying a ticket.
Like the Eurail Pass, as long as you know you are paying a price for the convenience. Just don't kid yourself that you are saving money.

Sam, I'm curious where you got the $424 pricing for the 3-day Flexi pass?
http://ricksteves.raileurope.com/rail-tickets-passes/swiss-pass/index.html - selecting first class 3 day flexi on this site is 340....? Are we looking at difference passes? I'll most likely be choosing second class and my age sort of helps b/c I can choose the Youth option (yay!). I also understand that there are some rules around "travel days" for the flexi pass. Technically, i wouldn't be traveling from BO to other places on Days 4&5 except up to Jungfrau...would that still count as a "travel day"??

Also looking at rail prices in Bernese Oberland on this site: http://www.jungfrau.ch/en/tourism/travel-information/tickets-rates/lauterbrunnen/fares-for-individual-travellers/.
One way from Lauter to Jungfrau is 92...i was actually thinking of riding up on the first train then, hike down afterwards...is that a good idea - is it scenic on the way down from Jungfrau?

TOTAL without pass = 331 or 238 (depending on one way or roundtrip for Jungfrau)
According to RS's website: http://ricksteves.raileurope.com/rail-tickets-passes/swiss-pass/index.html - a 4-day flexi for youth 2nd class = 255.
However, i would need to pay out of pocket for Jungfrau: 139 round trip or 69 one way...that should be it for out of pocket right??

Great that you can get the youth rate and I would also choose 2nd class. If you will complete travel by June 30, then you can use the Coupon Code SWISSEPASS20 to save 20% off the e-pass version of the 8-consecutive day pass at http://ricksteves.raileurope.com/rail-tickets-passes/swiss-pass/index.html. Youth price would normally be $323 US, or drops to about $259 after you apply the coupon code (before completing check out). That gives you 2 more days of maximum coverage than does the 4-day flexipass. The e-pass will be prevalidated for the 8-day window you choose, and you print it at home. You do need a return trip from Jungfraujoch, unless you plan to hike down the whole descent.

I thought that'd be a great deal too until I saw that it's for first class only... :(