Thank you to both, ofto and KQ321 for your detailed info. I will take a while to digest all that, plus playing with the booking site a bit to gain familiarity.

I am concern about Regensburg to Prague journey as it seems to invlove changing trains (or even bus) and different ticketing schemes etc..
The suggestion of having a beer enroute sounds great, but I am nervous about missing the train

I will have different currencies on hand. Not a big concern.

My time of travel can be flexible to accommodate the most straight forward (aka simple) journey. Avoid crowded train if possible. Are there such thing as "rush hours" on Regensbourg-Prague & Prague-Berlin segments?