Where would you go first

I agree about starting at the far end of your trip.
If you cut each stop down to 4 to 5 days, you could sufficiently see the city. It'd also allow you to stop in other great European cities along the way. I like:
Budapest
Vienna
Prague
Dresden
Berlin
Amsterdam
Bruges

Krakow is a little off the beaten path for this trip.

Your list looks fine. I prefer to start at the furthest point, so that there are fewer connections or shorter flights on the way back.

I think you will enjoy Kraków, I was there once and plan to go back soon.

I would start in Budapest, then Krakow, Prague, Berlin, Bruges, Amsterdam . Try to get a flight into Budapest and out of Amsterdam (or London if you end up tacking that on).
I did somewhat the same last summer in the reverse order, I flew into Brussels and out of Budapest.

Hello Wendy. When I choose my airline flight schedules for a Europe trip, I consider the airline flight departure times and flight arrival times. If I will travel from a city in Europe to my home, in one day, I do not want a flight departure time of 8:00 or earlier in the morning. And I do not want to arrive at my home late at night that day. If you will be at Europe a total of approximately 60 days, your flight in an airplane across the Atlantic Ocean toward the East could be in the day time. I do not know what are all of the day time flights that are convenient for you. I know of two airlines that have day time flights from The United States of America to the Heathrow airport of London in Great Britain. (I think you will have time for visiting London). American Airlines has an airplane departing from O'Hare airport of Chicago at approximately 9:10 A.M. It arrives at Heathrow airport of London at approximately 10:30 P.M. (England time). Shuttle busses go from Heathrow airport to hotels located near the airport. Some of those hotels are not expensive. I was a passenger in that flight, twice. I liked it. British Airways has an airplane departing from Kennedy airport of New York City (JFK airport) in the morning, and arriving at Heathrow airport of London in the evening. British Airways has an airplane departing from Dulles airport of Washington D.C . (the airport is located in the state Virginia) in the morning, and arriving at Heathrow airport of London in the early evening. A person starting at Toronto in Canada could fly to either Chicago or New York City, and be at a hotel in that city that night. And the next morning, fly to London. When I was a passenger in the day time flight to London from Chicago, I was in a hotel in Chicago the night before the flight from Chicago to London.

Hi Wendy. Okay, we're talkin' two months. Wow! So exciting for you.

If you can work in a stopover in Reykjavik, go for it. I'd choose to do it on the return trip because it will be warmer in June with sunset around 11.30 p.m.

Since weather is unpredictable, I don't know if that should be a major factor. Even so, I'd start as far south as possible (so Budapest) and work north, also because daylight hours will be longer in the south.

Budapest is a bit grittier so it might be a let-down at the end of a trip. One more good reason to start there. Don't get me wrong, I loved Budapest. It's a fascinating city with lots to see and do, and excellent day trips too. A week there will fly by.

Vienna (3 days is fine) is an obvious stop on the way to Prague (a week is a long time there), with possible side trips to Brno and Bratislava. Krakow is "out of the way" but you have time. You could fly from Vienna to Krakow then train to Prague. From Prague, stop for 1-2 nights in Dresden on the way to Berlin (minimum 1 week, if you like museums). From Berlin, train to Amsterdam (about 6 hours). From there, you can work your way around the Netherlands and Belgium.

Thanks for the suggestions. It confirms my first thought. I will look at adding Vienna maybe even Salzburg, the sound of music tour is kind of calling to me. The idea of a week I'm each city is just a guideline some places less for sure. I am a museum and history buff so any suggestions of additional stops will be great. I am heading to Paris this October so will not be going on this trip. My other thought is Luxembourg, not for a week but a day or two.

Wendy

It looks like you're focusing on Central Europe and environs. Lucky you - two months!

Amsterdam, as you probably already know, is one of the top cities in Europe for museums (along with Paris). IMHO, I would say that Berlin, Budapest and Prague, while very interesting from a historic viewpoint, are not known so much for their museums, generally speaking (disclaimer: I have not been to Berlin, but have a trip scheduled for there in October, so have been researching). Though I would highly recommend the Communist Museum in Prague and the Terror Museum in Budapest; I though they were very interesting. The museum of Cubist Art, if you like that kind of thing, in Prague, was good, especially when you follow it up with coffee and cake in their cafe (ideally on the balcony, so tourists can take pictures of you).

Bruges is just plain cute, but actually has a couple of nice museums and a reputed (disputed?) Bosch. A lot of people don't like Brussels, but my entire family really enjoyed the city, and the Art Museum is quite good. Several cities in the Netherlands and Belgium are worth seeing and have good museums or other locations of art, like the Ghent Altarpiece in Ghent (the Adoration of the Mystic Lam, by van Eyck), which has national significance to the Belgians.

Are you planning any time in the countryside? Especially for a trip of your length, you might consider mixing it up a bit by spending some time in a small town or village.

Enjoy!

I will forgive Lexma's statement about Berlin not being a museum city, since they said they haven't been there yet.

This is like the famous line from This Is Spinal Tap, about Boston not being a college town.

Berlin has many days' worth of wonderful museums, of every sort; certainly as many if not more than Amsterdam (not talking quality, just quantity). The German History Museum alone could take a full day.

Great information on museums and other sites. I am not sure yet if I will add any countryside stops. I am leaning to smaller town for a break or even just wondering days in some cities. Would you add Luxembourg to this trip, it looks nice but I'm not sure if I am leaning towards it as a place of interest or more an opportunity to add another country to my list. Dresden sounds interesting was not on my radar, but is now.

Wendy

I'd say start with Bruges and Amsterdam in April. The weather patterns there are maritime - it always rains but is rarely freezing.

By May things are getting nicer everywhere.

I'd probably then go Berlin, Prague, Krakow and Budapest (even though I normally try to work south to north in Spring) - because it seems the most logical order to put them in.