Looking for assistance in putting together this trip (2 week time span)- looking very complicated - thanks in advance
You need to ask specific questions if you want assistance.
It does not need to be complicated, all are junction points for trains day and night, Berlin to Krakow, Budapest to Krakow, Berlin to Vienna, Vienna to Krakow...all can be done on the night train, if you want to choose that option. What are your priorities? Foremost and least?
Skip Budapest. Substitute Prague.
David is right. Logistically easier.
Logistically, Krakow is a difficulty - there are fewer air connections and long overland rides (slow trains or buses). Use bahn.de for train schedules. I was in Krakow last week, then took an all-day bus to Budapest (where I am now). The bus was supposed to take 7 hours. The bus was a few minutes late getting into Krakow, so we left about 15-20 minutes late. Then we had a 15 minute delay because of some misbehaving passengers. We got to the outskirts of Budapest and then crawled through the city in rush hour traffic. And even then, the bus is less time than a train or flying. It's also cheap.
I enjoyed Krakow very much, but Prague would work much better for an itinerary, with good train connections Berlin to Prague to Vienna to Budapest. With Krakow rather than Prague in the mix, it looks like your itinerary would flow best with flights between Berlin, Krakow and Vienna and then train from Vienna to Budapest.
I'm a light sleeper so I never considered a night train.
Going to Krakow from Budapest or Vienna on the EN night train gets you in at Krakow Glowny bertween 0700 and 0730 hrs, very doable and direct.
If I can support you in making plan, I would like to use portals with trains timetables as http://rozklad-pkp.pl/en where you can find connections between Cracow, Budapest, Vienna and Berlin. It could be good idea to choose the extreme city by travel distance or time from these above for arrival by plane and fly away from the other end of your route - if it is not essential in flight price. All of these four cities have international airports.
For example you can start from Berlin and then have direct train to Vienna, then to Budapest and also direct one from Budapest to Cracow. The order could be inverted. And one more information, maybe you find it interesting. The train from Budapest to Cracow runs through Bratislava, a capital of Slovakia, so you can plan stop there to visit also this city.