Thanks so much, PalenQ! I spent a LOT of time on the phone today with Byron from BETS (BETS-European Rail Experts) and he explained all my options and confirmed that our itinerary is very feasible. I think we've decided to go with an 8-day, 4 country Eurail Select Saver Pass plus youth passes for the kids. That will cover all our trains within and between countries with the exception of one or two of the cheapest trips (Rome to Assisi and Salzburg to Vienna priced out as our cheapest, which is great since we can pay for Rome to Assisi up front and then know that if we have to pay in Salzburg that it won't break the bank.).
We'll pay separately for the train in Cinque Terre if our legs decide they've had enough.
We'll pay separately for the buses and cable cars in Switzerland, but only need to ride those once or twice each, since we'll do most of the region on foot.
Our campground fee includes a local bus pass for Bavaria, so we're set there as well.
The country-specific passes (Italian Flexi or SwissPass) don't end up making sense because our two most expensive days BY FAR are Italy to Switzerland and Switzerland to Germany and I assume that we'd need to buy those tickets separately from the country-specific passes. If that's NOT the case, please advise and we'll reconsider the Oberland Regional or SwissPass.
We'll confirm timetables on www.bahn.de/en to ensure our routes, but it's looking good and is still less than a car rental, which was into the thousands of dollars for a drop off in another country.
Thanks so much for all of your input, everyone!
Ann

Thank you, kitbag! The AirBnB reviews for the place we found in Biassa indicated that it was feasible to go to and from the Cinque Terre to the house by bus, but I will check the schedules and touch base with the host again to be sure. We plan to set out early in the AM, do the walk throughout the day, then train and bus back to Biassa and eat dinner there. The challenge we found is that none of the campgrounds in the Cinque Terre accept reservations for only 2 nights and I am not comfortable arriving without a reservation and two kids in tow. Any suggestions for reasonable accommodations within the 5 villages that we can reserve in advance would be most appreciated. :)

Instead of looking in the hills at towns that require buses, check to see what might be available in towns along the train line when it comes to AirBnb or hostels or campgrounds, even small hotels. Using the train you will have a much more flexibility, and even a 35 minute train ride will be simpler than depending on a mastery of the bus schedules. The trains run frequently, even later at night and quite early in the mornings.

Check out Airbnb or other alternative lodgings for the towns of Bonassola, Deiva Marina, Moneglia and even Framura (although the train sometimes skips that stop). Sestri Levante and Chiavari are not to far to go although they might be pricier -- upside is that you'll be well positioned to head onwards to Switzerland.

It's also worth checking out, if you haven't already, what Airbnb might have in La Spezia and even Levanto -- although lots of people compete to use these towns as bases for le Cinque Terre in high season.

Most of the towns I have mentioned have one part of town that is near the sea and the train station, and another part of town that it is up a mountainside, and you might need a bus to get between it and the train station. If you come across attractive lodgings at an attractive price, be sure to look at a map to see how close it is to the train station. You want to be within reasonable walking distance, or else you might as well keep your booking in Biassa.

Edited to add: This might work for you

http://www.campingfornacialmare.it/Campeggio-EN.htm

Kitbag, you have given the OP such good advice, I am posting just to remember your posts.

I agree with Sassafrass. So nice to have advice and not snark. I am so glad your trip is coming together. We stayed in La Spezia for Cinque Terre. An apartment at Crismar hotel.Two bedrooms and kitchen. We had a long day and it was easy for us to walk there from train. Hope the trails will be open, it was my favorite part of Italy, The hiking was big enough for one person only on some parts but people were polite.

Don't think anyone above has a problem with evening alcohol :-)
I do think chosing wisely in CT at the top of the season is tricky and if kitbag has the local knowledge then go with it.

My only alternative thought is to consider using the ferries to tour CT, less walking, prettier views and while there will still be crowds it will not be heaving unlike the trains.

I mentioned your posts, Kitbag, because they were so detailed and specific to the OP's needs in one part of the trip. Now, I am disappointed. Personally, I do not think any of the prior responses had been at all snarky. It is a long, complicated itinerary with a travel style that I would not even think of attempting, so I had no advice. However, other posters' concerns were all quite valid and they were all polite and helpful in expressing them.

I guess if you figure in the time difference he might be right. We get so many answers about googling Sassafrass and other off hand remarks that are best left ignored. Kitbag has offered some great advice.

The ferry: buyer beware: We bought the rt ticket but after we hiked we went to get on and it stopped the run back to La Spezia early in the day so we had to take the train. Check schedule very carefully. I think they were catering to the cruise pax and not the people actually staying there. The views from the water were ok but the best view was from the hiking trails. Those iconic photos you see of CT were there. La Spezia is the port for the ships.

most expensive days BY FAR are Italy to Switzerland and Switzerland to Germany and I assume that we'd need to buy those tickets separately from the country-specific passes.> Yes - a Swiss Pass would cover parts in Switzerland only.

Thanks very much for the specific advice, kitbag. I'll go back to our CT section and have a look at what might be able to changed. I understand that our itinerary looks very ambitious, so am not surprised or put off by folks who say so. I get it - it looks crazy and isn't how many people would like to travel, but it works for us and we appreciate the knowledge and input from total strangers who are willing to take time to help us out.
Thanks to all of you and keep the ideas coming! :)

Different strokes for different folks - like you I like to travel fast.

kitbag is fairly new here but his/her style rings a bell!