Swiss Travel Pass Flex

OK, I'll add in one more option. Get a 15 day Swiss Travel Pass. It is 440 chf vs 407 chf for the 8 day Flex Pass. That will cover you on day on day 2, with 50% discount on the Pilatus trip. It will also give free admission to a number of museums and free local transport in Luzern, Bern, Lausanne. Yes, Bern and Lausanne are covered by hotel cards, but it will simplify things.
You've done your homework, spreadsheet and all. You're coming to the conclusion that no matter what combination of passes you get, it is a small difference between them cost wise between all the options are toted up. The Swiss rails are going to get their money from you one way or the other.
Another option would be to just get a 120 chf one-month Half Fare Card. That means you'l be buying tickets ala carte so to speak, but it often yields the greatest savings.

Thank you Sam for your comments. It may look like the 15 day consecutive pass may just be simpler since I don't have to pay for the Lucerne day passes and also get 50% on the Schilthorn excursion which is 44.25CHF.

Alternatively I could use Flexipass on day 2 to get the 50% off on the Pilatus trip & save on the day zone ticket and pick one more day for the Flexipass which may work as well.

I gather from your comments that you actually need to have the pass "activated" in order to enjoy free access to museums is this correct? (i.e.If on day 4 I plan to visit Bourbaki Panorama and Rosengart and I am not using the Flexipass, I would need to pay for admission? If that's the case, I think it's almost a no brainer to get 15 day consecutive since on most days that I labeled that I do not need the Swiss pass, I am actually visiting places that I plan on getting in free with the pass.

Here is a list of covered museums. I see both the Bourbaki and Sammlung Rosengarten are on the list.
http://www.museumspass.ch/wp-content/uploads/2013/04/Museumsliste-01.03.2015-SBB.pdf

If you buy the pass ahead and it is open dated, you fill in your name and date of first use and have it initiated by the station ticket office before boarding the first train. You can also buy it at the ticket office at Geneva Airport train station (assume you are arriving by air there) and it will be already dated and have your name on it, so then you just show it along with your passport to any ticket inspector or museum ticket desk. Also when buying tickets with the 50% discount like Pilatus or Schilthorn trips.

I am coming up with approximately 432 CHF by purchasing the 120 CHF half fare card. This also doesn't include some buses and other museums/attractions that I need to pay - so I think the answer will probably be the 15 day consec. pass.

I haven't done any financial calculations for you, so I can't say which is the best deal. But something to be aware of is that if you get the 15 day pass, you get great convenience. You only need to line up to buy tickets for something not 100% covered. For EVERYTHING else, you just flash it when tickets are checked. I didn't fully appreciate how nice this would be before my trip, but I sure did during the trip. Particularly in the Berner Oberland, where I was frequently on trains, buses, and lifts, it was a nice "perk." So, if the cost is close, just get the pass.