Paris to Honfleur to Mont Saint Michel then back to Paris

Paris to Le Havre is best done by train from Gare Saint Lazare. The trains are very frequent and take about 2.5 hours. Then, there are regular buses to Honfleur across the impressive Normandie bridge (lines 20, 39 and 50, check out "busverts" website for times etc.); no need to arrange a ride.
After that, indeed, it's bus to Caen (again, look at "busverts") and train to Pontorson for Mont Saint Michel.
Mont Saint Michel to Paris is either by bus to Rennes, then train to Paris (you need separate tickets for the bus and the train), or by a cheaper bus-train combo via Villedieu-les-Poëles sold by SNCF (which might be seasonal, and might run as a single train rather than bus+train in high season).

This being said, 2 days at Mont Saint Michel is 1 day too long. Best to spend an extra night in Honfleur, from where you could visit another place on the coast such as Deauville/Trouville.

Balso,

Thank you for the detail insight to trains, buses and directions! It is much appreciated!

We went from Paris to Honfleur exactly as described by Balso....no problemo. Then bussed to Caen and got the train to Bayeux. again easy. Brad

It appears that the Le Havre bus station (Gare Routière) may have moved from just south of the main, end-of-the-line train station to just east of the penultimate train station (Le Havre-Graville station; bus station at 323 Boulevard de Léningrad). Can anyone confirm that this change has taken place?

I was in Le Havre for work two weeks ago for a day trip, I vaguely remember the bus stop still being right next to it.