Berlin-Budapest-Prague

A segment of our visit to Europe in early May will be from Berlin to Budapest, then from Budapest to Vienna, Prague, then to Frankfurt for the flight back to the US. Our question is concerning the order of visiting the cities and transportation for the two longest legs. Option 1: night train Berlin to Budapest (almost 18 hrs and a train change in Munichthis doesn't look good), Budapest for several days, train to Vienna, stay several days, train to Prague; stay several days, night train to Frankfurt ( 10+ hrs is doable but still change trains from Frankfurt Sud to Frankfurt Hbf at 5:00 AM). Option 2: night train Berlin to Vienna (14 hrsa little better but still one train change), then Vienna then Budapest, then to Prague and night train to FrankfurtOption 3: fly Berlin to Budapest and then same as Option 1. Option 4: fly Berlin to Budapest, then like Option 1 except fly Prague to Frankfurt.
We've not taken a night train before, (see post on transportation/night train trepidation) and would at least like to try a night train once (via first class deluxe 2 person compartment). Option 4 is the most humane, with Option 3 a possibility. We'd like some suggestions on flying from Berlin to Budapest and Prague to Frankfurt (reliable airlines, airlines to avoid, best time to fly, unpublished hassles at the airport, the culture of the train station and airport at 5:00 am, getting between the airport and the central train station in Berlin, Budapest and Prague, and times of day/night when it is difficult to get between the station and airport on public transportation and what is the Frankfurt Sud to Frankfurt Hbf about?). Thanks for reading.