You've obviously been to Europe before. Are you sure you're safe to drive after an overnight flight? I wouldn't be. I'm a zombie on my arrival day.
On weekdays I see trains for Caen scheduled to leave CDG at 9:46 AM and 12:38 PM that require a transfer at Le Mans, which would avoid the need to change train station in Paris. Caen is quite close to Bayeux; it's a short train ride away. There are reportedly multiple car-rental companies near the Caen train station.
Given how much driving time is involved in going from Bayeux to the D-Day beaches, I really cannot recommend a half-day tour, though the are offered by Overlord and possibly others. You just won't get much time actually at invasion sites if you don't take a full-day tour.
Everyone says Mont-Saint-Michel is absolutely overrun during day-tripping hours and that it is therefore best to spend the night there, seeing the island late on your arrival day and/or early the next morning. I have never been to MSM so cannot provide personal advice.
I use Skyscanner.com to research intra-European flights.