So confused

You're not alone in being confused by the wide array of Swiss Passes. I've even used an Excel spreadsheet to try and figure out the most cost effective pass, but usually just have to make an educated guess. Which pass to use will depend to a large extent on which trains, lifts, etc. you'll be using. You might find the RS Railpass page for Switzerland to be helpful - https://www.ricksteves.com/travel-tips/transportation/trains/switzerland-rail-passes .

For your time in the Berner Oberland, you may find that either the Berner Oberland or Jungfrau Regional Passes will be the best value. The Half Fare card is also a good option as that provides a discount on just about everything.

Good luck!

Yes, it is confusing, and to make it even worse, it changes every year! For instance, when I went in 2014, the trip up Mt. Pilatus was only partly covered by a Swiss Pass; new for 2017, it's now completely covered by a Swiss Pass (I just gave incorrect information on another thread!).

Ken is right, the only way is to make a list of all the trips you're definitely taking and possibly taking (and you've got a great head start above). Then, price them on the Swiss Rail website: http://www.sbb.ch/en/home.html But be careful; the first price listed will be with a Half Fare card, so you have to double it (if you're unsure, click and choose "no reduction"). The days you are not using it are irrelevant; if it's cheaper to get it for the trips you are definitely taking, get it. My trip was 10 nights, but for me the 15 day Swiss Pass worked best. Of course, some days I used much less than its daily average value of $49.20 - and other days I used much more.

"Due to the fact that there are so many lifts in this region to get to the many places (Gimmelwald, Murren, Schilthorn, etc.) are these included with my rail pass?"

Here's the map of what the Swiss Pass covers in 2017. Everything with a solid line is completely covered; most things with a dashed line are 50% off, except a few (like the Jungfraujoch) that are indicated with a circled number 1; they're 25% off. This is a PDF; scroll down to page 2 and enlarge as needed to see details: http://www.sbb.ch/content/dam/sbb/de/pdf/freizeit-ferien/ferien-kurztrips-schweiz/internationale-gaeste/sts-geltungsbereich_en.pdf

Here's a different pamphlet with more details and a variant of the map: http://www.swissrailways.com/sites/default/files/upload/documents/uebersichtskarte_2017_en.pdf

To answer your question directly, lifts up to Mürren and Gimmelwald are covered; lifts above this, such as the Allmendhubel and Schilthorn, are only partly covered. On the other side of the valley, trains to Wengen are covered; things above this, like the lift to Männlichen and the train to Kleine Scheidegg or Jungfraujoch, are partly covered.

You're right, in the Berner Oberland one is almost always going up or down something, so a pass really can pay off. In addition, it's a great convenience. You only have to buy tickets for things not fully covered; for everything else, you just hop on, and flash your pass when needed. If you're seeing museums in Luzern or Zurich, it covers many of them too - don't forget to add that in your cost calculations. Covered museum list is here: http://www.museumspass.ch/en/where-to-use-my-museum-pass/

On the other hand, if you're not sure about costs, you can always win with a Half Fare Card. It's good for 50% off everything that moves in the whole country, including the Jungfraujoch (only 25% off with other passes). Since the Card costs 120 CHF, if your total travel is more than 240 CHF, you can't lose. And even ticket machines have a half fare option, so it's easy to use - just not as convenient as not having to buy tickets at all.

"I've also heard that the weather in Zermatt is unpredictable, is it really in July?"

Yes - mountains make their own unpredictable weather year-round. My walking tour guide in Lausanne, in September, had just spent three days in Zermatt, and didn't see the Matterhorn fully even once. She said that this problem is unusual in September - but she had it, so there you are. So, one day in Zermatt is definitely taking a chance.

The Swiss Pass is so much more convenient than the 30-day Half-Fare Card, even if it does tend to cost a bit more. However, the more intensively you use the public transportation, the more likely the SP will actually be the more economical choice.

As Harold noted, as long as you plan to buy more than $240 in tickets the HFC will pay for itself. You have 9 full days in Switzerland, so best version of the SP for you would be the 8-day pass, second class, for $382.

I'm guessing you'll need to buy about $560 in full-fare point-to-point tickets for your itinerary, not counting intra-city buses, museums, or high mountain excursions. The $560 guess includes a bunch of round-trip back-and-forths in the Oberland region (you'll be going from Murren-to-Lauterbrunnen-to-X a lot). With the HFC this would cost you $400 including the cost of the card. With the 8-day second class SP it would cost you $382, assuming you don't start your pass until day 3.

And the SP includes admission to Swiss museums (including Trummelback Falls near Lauterbrunnen and Castle Chillon in Montreux). And it's so much more convenient because you don't have to buy any additional tickets except for the high mountain stuff such as the Schilthorn or Jungfraujoch.

The Swiss Travel Pass options are limited to 3, 4, 8, or 15 days, whether they run consecutively or spread over a month. So no handy option to pay for just 6, or 10, or 11.

Consider FastEddies' suggestion that an "8-day second class SP would cost you $382, assuming you don't start your pass until day 3." Definitely a possibility. But the pass for 15 consecutive days costs $83 more, versus the trip from the Italian border at Chiasso to Zurich costs 72 CHF, which is about the same. The longer pass could also cover transport or museums that you might use in Zurich on days 2 & 3.

If it's still a possibility, you might also consider doing the Swiss portion of the trip in reverse, starting closer to the Italian border. A ticket from Tirano to St. Moritz costs 32 CHF on the direct train. It seems like you would save a bit of north-south back-tracking and then be well positioned to travel from Zurich to Innsbruck, probably with an advance-discount RailJet ticket for the whole trip, not using the Swiss pass that day.

Thank you, Ken, for your detailed response. I'll definitely have to make a list and do a cost analysis.
Thank you, Harold, for the preciosity of your response. It's great to know that Mt. Pilatus is covered by the Swiss Travel Pass. I now realize the irrelevancy of unused travel days. The map is exactly what I needed and I appreciate the link you provided. I think the only lift beyond Murren that I would end up using is the Schilthorn. Potentially some of the other smaller lifts though such as the Allmendhubel. It's good to confirm with you that keeping the Zermatt portion of the trip flexible is important.
Thank you, FastEddie, for your response. It's good to have estimates and I'm glad the pass includes the various museums and sites I will be visiting. I think the 8 day pass is indeed what I will be leaning towards.
Thank you, Laura, for your response. I'm still considering doing the Swiss portion of my trip in reverse. I'm not entirely certain yet. I'm interested in know where you got the $382 figure from though since the websites I have looked at such as RailEurope have listed more expensive prices. I would be a 2nd class youth pass.