Berlin,Prague,Vienna, Zagreb, Dubrovnik, Sarajevo, Budapest, krakow

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We are just starting to put together an itinerary and we are creating two different plans.  The longer itinerary would be: Berlin, Prague, Vienna, Zagreb, Split, Dubrovnik, Mostar, Sarajevo, Budapest, and Krakow. A shorter version would be: Berlin, Prague, Vienna, Budapest, and Krakow.  Our plan is to travel by train.  I hope to pre-book our accommodations so I want to be able to predict departure and arrival times.  I am interested in the cheapest rates but I do find the railway websites a bit intimidating.  Your suggestions are most appreciated

A shorter version would be: Berlin, Prague, Vienna, Budapest, and Krakow.

If to stick to the mentioned 5 "core" destinations (and have particular set dates in mind), then your task is relatively easy. The key idea to save money traveling between the destinations in such case is usage of discounted tickets. Those called differently in different countries, but the general idea behind is that every railway company sell limited amount of ticket under specific offer much lower than a regular fare. Such discounted tickets save you a fortune in cases when you know your dates in advance (thus catch them before they are sold out) and have a chance to buy such tickets some time in advance.
For examples, Berlin-Prague tickets start from 29 EUR (seats), Prague-Vienna from 19 EUR (seats), Vienna-Budapest also from 19 EUR (seats) and Budapest-Krakow from 39 EUR (couchette). Thus basically in case you purchase all such tickets in advance (they all can be bought online from railways companies websites), your whole journey will cost you from 106 EUR (per person) in total, which is great price. But at the same time you need to consider the fact, that most of such discounted tickets are non-refundable and non-exchangeable (or can be changed, but it costs a lot to do it), thus any unplanned change in itinerary or you miss your train etc. and the money spent on such discounted tickets basically lost.
Regarding Croatia and BiH added to the itinerary, it is as well not a problem at all, you just need to purchase in advance ticket Vienna-Zagreb, while with segments Zagreb-Split and Mostar-Sarajevo you can just buy everything already on spot, since there is anyway no difference here regarding time of purchase. With Split-Dubrovnik and Dubrovnik-Mostar it's hard to travel by rail, since there is no railway in Dubrovnik, closest destination with railway connection is Ploce. Regarding Sarajevo-Budapest: direct ticket is a bit expensive (54 EUR) and no discounted tickets available, but it is possible to cut down expenses a bit if to "break" it via border.