Lane, first of all, it's wonderful that you're able to take a trip like this with your daughter. Due to a variety of circumstances, I've never been able to travel in the same way with my Sons.
To begin with, if you haven't already read Europe Through The Back Door, I'd recommend that you pick up a copy. It provides a LOT of information on travelling in Europe, including Itinerary planning. Pay particular attention to the "Rail Skills" section; you might want to download the free PDF Rail Guide from this website.
In looking at your "wish list", IMHO that's too many cities to comfortably see in 6-weeks (ie: so you don't feel like you've been "pulled behind the train"). I'd suggest adding a few places to the list and deleting some, until you reach a more "manageable" number. Keep in mind you'll have to allow for transportation times between cities.
Some of the other places you might want to have a look at are the Cinque Terre (Italy) and the Berner Oberland region (Switzerland), specifically the area around the small village of Gimmelwald. Have a look at Rick's shows on PBS (or perhaps order the DVD's) to see whether these might interest you. I noticed you don't have any stops in the U.K. listed?
As usual, I'd highly recommend using "open jaw" flights for best efficiency. It avoids the time and cost of returning to your starting point. Note that you'll lose your first day in flight times and time zone changes (esp. from the west coast), so be sure to allow for that.
Try to plan your route in a somewhat logical sequence, so that you don't do any "backtracking". Don't spend too much time on transportation until you have a rough idea of your Itinerary and order of cities. Rail is usually the least expensive, however for longer legs budget flights are more efficient (however there's a few "pitfalls" to be aware of with the budget carriers - more on that later if you need details).
continued......