For large stations like Zurich I would allow one hour.. This gives a margin for late running and time to become familiar with the station layout. Zurich has two levels! With a family you are not going to be able to get off your inward train and navigate the crowds across the concourse! Someone who know the station well could do it in much less time. There are two trains an hour from Zurich to Luzern so just get on the first one you can make. I’d allow at least thirty minutes at other interchange points. 

For alternative routes/times use the journey planners and maps of the country you are travelling in. The RailPlanner app is a good start but NEVER rely on it as it is not updated on a daily basis.

I don’t understand the third question.

1.

In Zürich, it's possible to do the change in 8 minutes. But it's indeed the fact that the direct trains from München arrive in the underground part of the station and you need to go upstairs. But: The connecting train to Luzern runs every 30 minutes and you'd need no reservation. So if you are too slowly you'll loose just 30 minutes. So it's not a problem at all. No need to plan ahead. It's a little bit different in Mulhouse, because there may be not that much connections to Dijon if you miss the train. But it's not a very big station so 14 minutes shouldn't be a problem. The former train starts in Basel and it's not a long jourmey where delays are common.  

2.

Your best bet is: Use the travel planner of the country you are travelling in. It has the most reliable changing times. For instance, in Switzerland they may be very short (sometimes just 2 or 3 minutes) and they work. But it really depends on the country. In other countries you may need much longer changing times. 

3.

It depends. If your connecting train has no mandatory reservation (see München to Luzern), you may just hop on the next one. If it has, you'd normally need a new reservation (free of charge). So it's mainly not a question if it's a pass or a single ticket (single tickets may also be flexible to use or not). It depends on train and country, too. 

Hope this helps at least a little bit. 

Yes, this of hektor is just fine-would have written same-same.

@3: in case of missed connection THAT railway you are then at has the obligation to help you out-and for further onward travel with that pass-you will never be obliged to then pay for normal tickets. BUT-if these trains are all with mandatory RES it may be a problem if all trains are very full-f.e. in FR the SNCF then often gives you ´places debout/strapontin´ seats= fold down seats in the entry-halls-and you can claim any unused normal seats later (after 10-15 mins the signs lapse and it gets free for everyone-untill next stop only! But this really varies an enormous lot per country and how flexible or welcoming they are-one of the main downsides in fact for INTerntioanl train travel

Thank you, everyone for your responses.  This gives me a better idea of the situation on the ground.  I will continue to research the best times and book soon.  Will ask again if I need more guidance.  vielen dank / merci beaucoup !

For domestic train in Germany and Switzerland you don't need any reservation so there's no need to make reservations from München to Zürich.

Thank you, AnnaB !  But just to check my understanding : I should still book tickets in advance from Munich “through” to Lucerne ?  I just don’t need to reserve seats, and if I miss the first connecting train at Zurich, then I can catch the next one to Lucerne without waiting too long ?

Your pass is your ticket, so there's no need to book anything. You just need to register your journey in the app, or write the train in the travel diary (paper pass).

If you miss a train, then you can just delete it from My Trip and add the one you will take. On a paper pass, you just write a new line (I generally only write a line shortly before boarding a train).

@Alvin Sim Are you planning to use a Eurail pass or just to buy normal tickets?

From what I have read on various websites and blogs, I’m more minded to buy normal tickets because I have a fixed, fairly low number of train journeys (7); any side trips not confirmed), and am only visiting a fixed number of cities/towns (7).

@Alvin Sim When do you plan to travel? Where are you planning to travel?

Have you calculated the cost for normal tickets compared to the cost for a pass and any needed reservations?

Thanks AnnaB.  I have compared the cost for normal tickets (7 main journeys) vs the cost of a pass/reservations a couple of times. We are travelling a loop starting/ending in Paris, with 2 places in France, 3 places in southern Germany and 1 place in Switzerland. Seems like it’s about the same cost, with normal tickets possibly slightly less.  Thanks again.

Ok. If the price is about the same, then I'd go for a Eurail pass as that gives more flexibility.