1. Stuttgart-Munich (Monday) We might like to stop in Dachau - how would we book this, or can we get off and resume our ticket?
Well, here you have two options: a) when searching for connection on DB website just enter intermediate stop (and time length of the stop) like this -->
German Railways allow a stopover with a discounted tickets, so all 3 can still travel for as low as 29 euro in total, which is a good price; b) if you want full flexibility, then don't bother with any in advance purchase, but simply opt for
Quer-durchs-Land-Ticket ticket, you can buy it before departure and use whole day long, thus will allow you make as many stopovers as you like
2. Munich-Paris (Option A) Night train Tuesday; (Option B) morning train Wednesday. I am not sure which Paris station to choose. We will likely get a car service to take us to our rental. Do you recommend the night train? We would want to book the 3 person bed option. Otherwise like to take a high speed train in the morning.
Both overnight CNL train and daytime direct high-speed trains arrive to Paris East (Paris Est) station. CNL train takes more than 10 hours, but saves you half of the day time and hotel night, with high-speed it's 6 hours travel time.
Hard to say what might be more preferable in your case, so maybe it makes sense just to check options for you date and than make a decision. For instance if high-speed train will be much cheaper, than why not to choose it etc.
3. Paris-Stuttgart (Saturday)
Idea here is the same, just visit both DB and tgv.europe websites and see what both have to offer, sometimes one is cheaper than the other, even for the same connection. Generally to Stuttgart there are more direct connections from Paris, so the fare should be better comparing to Munich-Paris connections
We will also do regional travel such as Munich to visit Neuschwanstein, Paris to Versailles; and use Metros for travel around the cities. Should we buy those types of tickets once in the city we will be based in?
Well, Versailles is rather close to Paris, so there is nothing to invent here, just use local transport and buy tickets on spot (
Transilien is of help here), but with trips like Munich-Fussen-Neuschwanstein it might be a good idea to get a
Bavaria Lander Ticket, which is the same thing as Quer-durchs-Land-Ticket, but only on regional level and cheaper.