Your locations dont work hugely well, I m afraid. Salzburg is east from Munich, Fuessen west, and Cochem well north beyond Bavaria. If you go by train, I might suggest using M as base and doing day trips to S and F, then moving to C.
But I suspect you ll drive.. However I d still suggest starting with a couple of days in M to get over jetlag. From S drive on alpenstrasse to F, which will take s day with stops. It wont be warm weather, so you may want to bear in mind indoor things where possible. Between S and F is Mittenwald, which allows cable car or chairlift.
Near S is Koenigssee a lake with excellent electric boat tours all year roundEdited: 3:55 am, November 21, 2013
A Bavaria Ticket means your entire family can travel anywhere within Bavaria for 30€ per day - short trips or long trips, you're covered as far south as Füssen and Salzburg, and nearly to Frankfurt in the north (which is only 20 miles from the Bavarian border.)
What sort of activities do you have in mind? Biking? Zoos? Open-air museums? I would suggest that you consider first which family-friendly activities you will pursue and the weather in places that offer those activities - and then determine your destinations. 11 days is a nice amount of time, but as ethelman 2 points out, your destinations are sort of all over the place.
The Alps tend to be weather-problematic at that time of year for outdoor activities - lots of wetness. I'd be tempted to focus on points from Munich north instead if you hope to get outdoors. In the Frankfurt area, March and April typically have the smallest rainfall totals of all the months.
So you might consider looking into the sorts of activities that appeal to you in just 2 areas - in and around Cochem, and in northern Bavaria (which is really close to Frankfurt) - Nuremberg, Bamberg, Würzburg, Rothenburg, and numerous other smaller towns are popular destinations in this area. If Munich is a definite, MUC and FRA should work well for you. You might even use just FRA if Munich isn't a must. 5-6 days in two areas would be nice - rent an apartment in each spot and head out on daytrips. Or include Munich and spend 3 days in Munich, 4 in No. Bavaria, 4 in Cochem.Edited: 9:15 am, November 21, 2013
Check and see if any sommerrodelbahn are open that time of year. I know there are ones near Salzburg and Fussen
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