Presumably you will be taking the ferry with a car. If not, good luck for getting around! Best would be to take the Brittany ferries Portsmouth Caen and back from St. Malo to Portsmouth or vice versa. That way you'd be driving just in one direction and not going backwards & forwards. Where you stay depends on your ferry times. If 2 nights is all you have it sounds like a big rush. Could you take a night ferry which would add 3rd even 4th nights?
If you don't have a car , you should go to Cherbourg from where you can get the train to Bayeux. From bayeux ypu can take minibus tours of the d-day beaches and the Churchill shuttle to MSM.
if you have a car: Bayeux
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