"ludwicks castles" - not a day trip I especially recommend from Munich. Yes, I know, it's heresy to suggest not going there. But it takes 5 hours by on trains and buses to get to N'stein and back, all for a 30-minute tour, not of a real castle, but of a palatial, late 19th-century home. What's the allure of N'stein? Its "importance" to most tourists lies in the fact that N'stein was one of several buildings Walt Disney's architects borrowed from to design Disneyland's Cinderella Castle - in other words, hordes of international tourists go there to see the fake castle - often believing it's some genuine-article castle - that inspired another fake castle.
There are some interesting rooms there, but I would suggest that you are already logging considerable ground miles and that it would be more conserving of your limited time and maybe more interesting to pay a visit to Nymphenburg Palace, which is right in Munich and which has been around for centuries longer and seen much more history. It was Ludwig's first home (he was born there) and also home to many other important figures in German history. The only real resident of N'stein was Ludwig II - and he lived there for only 6 months.
Nymphenburg: http://www.schloss-nymphenburg.de/englisch/palace/
Day trips from Würzburg, some mentioned above: Iphofen, Ochsenfurt, Marktbreit, Nuremberg, Bad Windsheim (for a superb open-air cultural museum.)
Franconian Open-Land Museum
Touristy (2.5 million per year) Rothenburg is another option, but I found the less trampled towns mentioned above more enjoyable - these towns are far less tourist-oriented, places where there are other goals besides selling stuff to tourists (Iphofen, for example, is a wine town: "Gypsum, wood and wine... these are our pride" is the town's motto:
http://www.iphofen.de/download/ortsprospekt_englisch_100510.pdf