Honeymoon/Family Vacation

I would suggest cutting some of those places off your trip. At that pace you'll constantly be getting on and off transportation. Save some stuff for later.

What I would say is limit yourself to perhaps the following itinerary:

London-Paris-Avingnon or Switzerland-flight to Rome-Florence-Venice. Remember you can always come back!

I am not good at outlining itineraries , but I have some ideas.
First, for each place you have written down , jot down reason or attraction to place, ie London=Tower of London, British Museum , London Eye, and Paris " Eiffel Tower, Notre Dame, Boat Cruise, Arc De Triomphe , Louvre, Versailles , Bike tour and Venice= Canals, ride in Gondola, see ST Marks square etc etc.
Now, anyplace that has only one or two things, drop. It is better to spend 4 or 5 days in 4 or 5 great places, then to spend 2 days in each spot.

Personally Florence is a snooze fest to me.
Prague sounds great , but its out of the loop and you probaly don't even has any specific ideas of why you want to go there except everyone says it gorgeous( which it likely is, but we are trying to pare down your list) .
Rome has tons of history, so does Paris, so in my mind they are worth at least 4 days each, if not more.My 12 yr old can't wait to see the Coliseum!

Please google Fat Tire Bike tours, your son would

love to do them and so would you!! One day tour or night tour of Paris, really fun.

I like the idea of building in some beach time, I mean kids like beaches and one can only take so many museums and monuments..I have only done the south of France once and that was years ago, so hopefully soneelse can jump in there and suggest a good beach stop.

Well, just build your itinerary around the major train routes: London to Paris is no problem. Then there's a choice of three routes: 1) Paris via Strasbourg and Stuttgart to Munich. 2) Paris via Heidelberg and Frankfurt to Nuremberg. 3) Paris via Brussels to Cologne or Amsterdam. There also is a high-speed route from Amsterdam via Düsseldorf and Cologne to Frankfurt an on to Nuremberg and Munich. From Cologne there are cheap flights on germanwings.com or CSA Czech Airlines to Prague. The Rhine river valley with the world's highes density of medieval castles is between Cologne and Frankfurt and I'm sure your son would love to visit a real knights' castle! From Munich (visit the Neuschwanstein castle by Füssen) there's easy access to Milan and Venice...