Geneva then to Berner Oberland-rather than Munich to Zurich then Berner O?

I'd book the flight into Geneva and out of Munich so there is no back tracking.

So, just so I'm clear. NJ to Geneva is that a separate option? So you wouldn't go to Munich and Salzburg? I liked both those cities a lot and they both have interesting and beautiful buildings and churches, good people, good brew and places to wander. In terms of Geneva, I'd stay in Vevey or perhaps Lausanne. Vevey area is known for wine.

In BO, I'd highly recommend a stop in adorable Gimmelwald to try their brew and enjoy the view right in the peaks of the alps.

Berner Oberland ("Rough Guide" says Bernese)

The first is in the language of the area.

The second, first word Bernese - is in English - second word Oberland - is in German, a mixture.

Or do the Rough Guide use a different phrase for Oberland?

We spend our summers in the Alps every year and are getting ready to make a similar treck as you so I've done a decent amount of research on the options. We're flying into Munich, renting a car to spend a month in Austria and then returning the car to Munich to train from Munich to the Berner Oberland where we stay for 2 months.

If you want to do the first option of getting from Munich to the BO, there are 2 or 3 direct trains from Munich to Zurich a day. I think I've calculated for us leaving on the 12:55 train from Munich will get us into Murren around 7:30 or 8:00 pm. A long day but not too crazy.

You may want to look into renting a car for the first portion in Germany/Austria. I'm a big fan of trains in Switzerland but you can see more if you have a car in Austria. For example, if you're interested in Salzburg, having a car allows you to explore out in the Salzkammergut (lake district) of Austria, which is stunning -- things like Konigsee, Berchtesgaden, Hallstatt, Wolfgangsee, Mondsee, etc. etc. You can then drop your car off at the Munich train station and train for the rest of the trip. AutoEurope only charged us something like a $30 extra fee to pick up the car at the Munich airport but drop it off at the Munich central train station.

Another option is to look into what the drop off fee would be to rent your car in Munich, explore Austria and then drive to Switzerland and drop the car off in Interlaken. Then use trains for your portion of the trip in the Berner Oberland. We've done this a couple times when trains from our previous destination weren't an option. It is more expensive, but could save you some logistics to just drive the car to Switzerland to drop it off and not have to think about the transition. Sometimes that convenience can be worth the money on a logistics/transition day. It also allows you to see parts of Austria/Switzerland that you wouldn't otherwise see on the drive. The rental car drop off is at a hotel in Interlaken and then you walk about 10 minutes to the train station to continue on to wherever you're staying in the BO.

As above poster mentioned, for sure have a Schwarz Monch beer at Pension Gimmelwald. If you like hiking, do the North Face hike from the Allmendhubel above Murren down to Gimmelwald and end with a beer at the Pension.

If I was planning your trip I'd probably do something like this:
Day 1 - Fly into Munich, rent a car to drive to Salzburg or somewhere to stay on a lake in the Salzkammergut
Day 2 - Salzburg/Salzkammergut
Day 3 - Salzburg/Salzkammergut
Day 4 - Salzburg/Salzkammergut
Day 5 - Drive back to Munich
Day 6 - Munich
Day 7 - Munich
Day 8 - Train Munich to Berner Oberland
Day 9-15 - Berner Oberland
Day 16 - Fly out of Zurich or Geneva (Zurich is slightly closer)

We flew from Barcelona to Geneva and then took a train to Bern, stayed the night, then continued on to Murren. Was pretty easy. Geneva was a much smaller airport than Zurich.