For travel between Munich and Lübeck flying makes a lot of sense, especially if you are at Munich Airport already.

Wuppertal is less than an hour from DUS, so flying MUC-DUS is a reasonable way of getting from Munich to Wuppertal (though you wouldn't save an awful lot of time over the train journey).

For travelling between Lübeck and Wuppertal, however, the train is really the only sensible option as flying would take longer!

Taking the bus to the marzipan factory is easy - No 7 or No 15, journey time about 20 minutes.