That's a long time to spend in Frankfurt. Just my opinion of course, but I don't find Frankfurt (essentially a big, ugly financial center) too appealing for more than a day. I think you might do better spending that time in/around Munich. Another option is taking the train about halfway to Munich (to Nürnberg) and spending a day or two there, then continuing on to Munich.
Q4: No issues, but try to get on a direct train to Munich (or Nürnberg) instead anything that requires changes. For more comfort, speed and a guaranteed seat, stick with the ICE or IC trains as opposed to the regionals.
Q5: One good way to spend a day is at the Deutsches Museum, which is right off the S-bahn line in downtown Munich. I like going to the Englischer Garten and having a beer by the Chinese tower (easily reached by bus). There are also the Alte and Neue Pinakotek art museums that are worth a look. Munich has a zoo as well that the family might enjoy (as does Nürnberg).
Hope this helps a little.