Suzanne,
That's a bit of a challenging Itinerary, but it should be possible to fit-in most of your wish list. Perhaps something like this would work.....
- Flight inbound Venice
- Train from Venice to Varenna (Lago di Como) - one of the shortest travel times is 4H:33M, with one change at Milano Centrale.
- Train from Varenna to Lucerne (the best option looks to be a departure from Varenna at 08:37, arriving Milan at 09:40 - from there connect to a departure from Milan at 10:25, arriving Lucerne at 14:20, one change at Arth-Goldau).
- Train from Lucerne to Berner Oberland (travel time will be 1H:50M to Interlaken Ost, another 20 minutes to Lauterbrunnen and after that the time will depend on which town you have chosen to stay in - Lauterbrunnen is the most central to both sides of the valley and also the transportation hub).
- Train from Berner Oberland to Munich (this will be a longer travel day - one of the shortest trips is a departure from Interlaken Ost at 08:00, arriving Munich at 15:11, one change at Karlsruhe).
- From Munich you can easily travel to Salzburg for a few days and make a day trip to Hallstatt or spend a night or two there.
Keep in mind rail schedules can change so this is just a guideline.
There are lots of ways this could be arranged, and this is only one suggestion. While 17 days is a good time frame, you probably won't be able to see everything on your list unless you want to spend a lot of time looking at the sights through the windows of a train. Also, with two young children I'd suggest a more relaxed Itinerary, where you can enjoy the places you've come to see.
I'd suggest using fast trains wherever possible, as that will not only be faster and more efficient, but will avoid the usual issues of I.D.P.'s, ZTL's (limited traffic areas - high fines), high fuel costs, parking, insurance, tolls, etc. No car can travel at 300 km/h, which is the speed of some of the fast trains.
Although you've been to Innsbruck, you might find it helpful to read Europe Through The Back Door prior to the trip. After that use the country or city-specific guidebooks to plan hotels, sightseeing and other details.
Good luck with your planning!