Well, that sure is a whole lot of cycling! And a lot of time!
Amsterdam to Prague is pretty much the opposite direction to Netherlands south down to France! :-)
Ev6 is the hilly one!
I've done most of those with the exception of the Berlin/Prague part.
Some comments:
Personally, I wouldn't cycle Amsterdam to Berlin. Nothing wrong with it, but there's more attractive places out there.
The Rhine is great, but some parts are definitely better than others. Specifically, the section from Cologne down to Mainz is probably the most scenic and the most along the river.
Ditto the Danube. By far the most popular (and busiest) is Passau to Vienna. Glorious! After Budapest and heading for the Black Sea it is a lot less developed.
(It's entirely possible to link the Rhine & Danube routes in Switzerland).
France is great to cycle through, but I wouldn't be a slave to an EV route.
With a bit of planning it's possible to create a pretty impressive circular tour covering a lot of what you want to do - but it'll be months on the road.
Here's a handy hint: Using cycle.travel, create an account and start creating simple routes such as Amsterdam to Berlin. Create a few routes like this forming a rough circle. Put all those routes in one folder (max 20) and when you click on the "map" icon, all the routes will be presented on one European map.
If you go back in and fill preferences like average speed etc. each route on the map will give you estimated mileage and time to complete. You can then go back and look at routes in detail or add alternatives to see which suit the best.
Don't forget there are lots of local routes that are just as well developed (and sometimes better than) the EV routes. In fact, I've just added one to my wishlist - The Iron Curtain trail, basically a route along the old West/East border in Germany.
Biroto is useful for those as are the likes of RWGPS and cycle.travel - in fact any planner that allows you to search other people's routes.
As always, have a look on CrazyGuyOnABike for others who have done similar.
Have fun!