Heading to Amsterdam and beyond and really sort of paralyzed trying to figure all this out...

You won't get bored if your idea of fun is riding trains all day. You land on the 6th and leaving on the 12 for London, leaving just 5 full days between Amsterdam and Paris. 5 days is a good amount of time for Paris alone. You bought your airline tickets already, leaving you the awkward return to Amsterdam for your flight home.

You might try this. Go to Brussels straight from Schipol airport after you land on the IC train. Stay 2 nights with your second day to Bruges for the day. Then take the Eurostar to Paris and stay 4 nights. You will need reservations for that. Then fly from Edinburgh to AMS on the 18th and spend 3 nights in Amsterdam before flying home

In the Netherlands, don't worry about getting bored in one spot, if you feel you need something else to do, you can daytrip to a big chunk of the country in under an hour. If you want to be in Amsterdam proper, book a place now. Otherwise, maybe someplace like Leiden would be good, close to the airport, easy train rides to Amsterdam, Delft, Haarlem, Den Haag, Rotterdam, and more.

As for overall schedule, Amsterdam, someplace in Belgium, Paris, and London are plenty for two weeks. Probably need to book trains, Eurostar, from Paris to London, and London to Amsterdam now, even with Eurail, you will need a supplement. You could also save Belgium for on the way back to Amsterdam for your flight, Taking the Eurostar from London to Brussels instead. For Belgium, maybe consider Ghent as a base.

Forget Scotland, no time, no need to go to Luxembourg on this trip, Germany, even just zipping to Cologne might be too much.

Well there is a way this might work out better. We do land on the 6th and have Anne Frank reservations for the 7th. We can leave on the 8th and go straight to Paris and have 4 nights there, traveling to London on the 5th day (the 12th). Then 4 nights in London and make out way back to Brussels for 4 nights and do the little cities like Bruges and Ghent as separate day trips. Then one last night in Amsterdam.

So basically stick that time in Belgium on the back end.

I guess I wasn't paying enough attention to Paris because I've spent a fair amount of time there. But my daughter hasn't.

Edit: Paul you were just typing exactly what I was ;-) Is it pretty easy to get back to Amsterdam from Brussels or Ghent?

I'm not going to rent a car in Paris or London as their public transportation is good and we'll be in-city for most of the time.

But for the time in Belgium I foresee day-tripping to places like Bruges and Ghent, etc. Would you guys suggest renting a car those four days?

Matt,
I hope you get your lodging reservations for Paris soon. The Olympics are bringing lots of people to Paris (all the attendant personnel for the teams, lots of extra media people, and of course attendees, as well as athletes). Many of them will arrive in June. Lodging prices have gone way up because of this, and some sights in the city will be affected by the preparations. Your final plan sounds much better than the first one.
Have a great time, but be sure not to spend too much time going from city to city. Enjoy yourselves!

A car would be a terrible idea in Belgium. Trains are very frequent, avoiding hassles like traffic congestion, expensive parking.

Good to know, thanks. It wasn't clear to me that trains were good for day-tripping to nearby cities.