Next month I would like to visit the following cities from Paris:
Rouen, Honfleur, Normandy D-Day Beaches (Bayeaux?)
I would like to stay overnite in Honfleur and Bayeaux. If I were to take a train from Paris to the first city in Normandy, and rent a car from there, which city should I hit first? Rouen , then Honfleur then Bayeaux???\Thanks

Your plan seems logical to me. To get from Rouen to Honfleur by public transportation would mean taking a train to Le Havre and a bus from there to Honfleur. Note the correct spelling: Bayeux.

Rouen is so close to Paris that in my opinion it is easier to drive out of Paris. Gare du Nord is a good location--the garage is right below the rental agencies, and after two turns coming out of the garage it's a straight shot to the highway [Porte de la Chapelle]. Viamichelin's driving time estimate is 1.5 hours.

I would take a train from Paris to Caen and then rent a car.

If skipping Rouen and heading to Honfleur, one would be better off taking a train to Deauville and renting a car there. You can leave Paris at 8am, get there in two hours. There is another direct train in the afternoon.

Renting a car in Caen worked great for me a few years ago. I stayed two nights in Bayeux but car options were better in Caen. I had a great time driving in Normandy - very easy.