Wow. Looks like a great trip.
Maybe take a day off Amsterdam, and add it to Berlin?
For the leg in Spain, will you go to Portugal from Madrid by train? Salamanca and/or Sevilla would make great side or day trips out of Madrid.
Vueling Airlines has cheap flights to/from Spain/Portugal/France, but the more ahead of time you purchase, the cheaper they are, and you probably do not want to lock yourself down with flight dates.

Yeah that would probably be a good idea to spend an extra day in Berlin. Any advice on what I should look to see/do in Berlin?

As for the trip from Spain to Portugal I was planning on going from Madrid by train. I’ll look into those places you mentioned. Are they both somewhat similar to each other?

I was thinking about using flights, but like you said I don’t know if I want to be locked down that far in advance. Could help cut travel times if I were to find cheap flights at the last minute though.

Thanks for the advice!

Flights can help save time, but remember to figure the full cost and full amount of time involved in a flight. Typically, any flight takes nearly 5 hours, city center to city center. That’s 45 minutes to the airport (airport transportation generally leaves from the train station so that’s in addition to total time for a train ride) 2 hour advance check-in/security, 1 hour flight time, 45 minutes to get into town from the airport. An afternoon flight effectively kills the entire day for sightseeing. Most itineraries end up with lots of 4 to 6 hour train rides…

Thanks for the advice Oldlady. I didn’t take into consideration all the time that would be wasted for the process both leading up and after the flight. Night trains will probably be a common method of travel for me as I can sleep on the train and wake up when I get to my destination. Shorter trips I’ll just have to do in the early morning so I can arrive at a decent time and be on my way.