To answer our questions in a slightly random order. Prague is perfectly safe for two women - I went with my mum last year. The only provisos I would make is that it does get rowdy late at night so I would avoid being out after about 10pm if you aren't comfortable in that environment (though it is fairly safe). And as Prague gets very crowded there is, as To go says, a risk of pick-pocketing. But then that is the case in every major city and I don't think Prague is especially bad.

Your plan sounds sensible and achievable so no problems there.

I have taken that overnight train, albeit in the opposite direction and the portion that starts in Copenhagen rather than Amsterdam. The views along the Elbe are stunning. The compartments in question are pretty comfy (our train had coaches that were pretty new but the older ones are ok two). No security concerns about the train journey and the crew tend to be lovely - they all speak English.

Link to a report on our trip which includes a picture of our compartment set up for breakfast and some of what we did in Prague (the first bit isn't relevant to you as we started in Sweden) http://www.holidays4heroes.org/2013/...s-of-europe-2/