Looks like a good trip. You're using the train and car the right way, for the Rouen to Bayeux leg. That way you have the car's flexibility to see the D-Day Beaches the way you want; but you'll want to closely research the D-Day Beaches, since you're not taking a tour. I've done it the way you're doing it.
2 nights in Rouen would give you one full day there. But I'm not sure you need 2 nights there, or that you have that many nights available. If you do 1 night that will of course give you only a partial day in Rouen.
I'd take a close look at what's in Rouen and then decide whether you want a partial day there or a full day (which will mean 2 hotel nights). I've done one night there and a partial day there and had enough time to see the highlights of the historical core area: the cathedral (if you remember Monet's paintings of it!), horloge, Joan d'Arc execution sight and memorial. And a nice dinner.
Driving in and out of Rouen can be challenging, esp. since that will be your first day with the car. You can avoid some of the traffic hassle by sleeping on the outskirts instead of in the historic core, but then you have a problem getting into the historic core for sight-seeing.
IMO spending a night in Mont St. Michel is special, on the island I mean. There are limited hotel rooms on the island so I'd book that lodging as soon as you know your dates. The island is magical at night after the day-time hordes have left, which is by about 6pm.
I'd do Honfleur instead of Caen (they are very different places). Caen is a bigger city, was bombed heavily by the Allies in WW2, so many "historical" structures are rebuilt after the war, that's my impression, but I haven't spent much time in Caen so that's just my guess, I could be wrong. It does have some D-Day and Normandy fighting sights/museums, but I think you'll see that on the Bayeux and D-Day Beaches portion of your itinerary.
You'll be glad to have the car to explore the Loire chateaus, but you'll want to pay attention to where you sleep, in some of the towns, though they're smaller, parking can be a hassle if you're sleeping in a place that's not car-friendly, for example, a hotel in a pedestrian zone.