I agree with everyone who has said to go with some variation of option 3 with Berlin added on. I've done different parts of that trip at different times, and absolutely loved Berlin, Prague and Budapest. Amsterdam isn't close enough to make it worth visiting in this trip if you're committed to rail travel, but you can usually play around with flights so that you'll have an 8-12 hour layover there, which I highly (no pun intended) recommend.
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