Judy, as you aren't arriving in Bayeux until 15:00, getting to Mont Saint Michel on that same day is going to be very difficult. One of the rail experts here can provide the details, but as I recall it involves a train and a Bus ride to get to Mt. Saint Michel.
One possibility might be to rent a Car in Bayeux, as that would be the most direct method. There is at least one car rental location in Bayeux, but last time I rented there, the staff spoke only French (your Hotel may be able to set that up for you). I haven't checked the driving times there and back, but a GPS unit would be a really good idea.
For your trip from Bayeux to the Museum in Caen, you might check the bahn.de or SNCF websites to get the times for trains that will get you there by 09:00. One suggestion though - Bayeux doesn't have a lot of Taxis, so I'd suggest getting your Hotel to pre-arrange one for the morning you'll be going to the station. On the way back, there are usually Taxis at the station to meet arriving trains.
It's not surprising that BattleBus is fully booked for June 1-4. That's just before the 65th Anniversary ceremonies, and they usually like to take some time off themselves to attend. I'm surprised you were able to get a Hotel booking at that time of the year?
Bayeux is an awesome town to stay in! Be sure to see the Bayeux Tapestry. One other point to mention (if you haven't travelled in France before) is that the restaurants don't usually open until about 20:00 although L'Europe and some others can provide meals earlier (upstairs). Check the France Guidebook for restaurant listings, as there are some really nice restaurants in Bayeux. If your budget will allow a "splurge", try Le Pommier.
Happy travels!
