I've never been to the museum in Caen, though from what I understand it's an excellent museum that can easily occupy several hours of your time. However, since you're devoting a full day to DDay sites already (Day 2) then I'd suggest other alternatives. Sure, Deauville is lovely but even lovelier is Trouville (IMO) which is right across the harbor from Deauville (they are separated by a harbor so you easily cross the bridge and walk between them). You could easily spend 1-3 hours walking around Honfleur and 1-3 hours walking around Deauville/Trouville without visiting any type of museum. Also, allow yourself time in one of those places to eat, whether that be sitting down at a restaurant or grabbing a sandwich from a boulangerie for something quick.
Since you'll have a car then an alternative you could consider would be doing a scenic countryside drive through the Pays d'Auge region south of Deauville/Trouville. This is cheese and cidre country (if those things interest you) but it is also a lovely place to wander on scenic country roads and stop from time to time to spend a few minutes walking around charming villages.
To do this get yourself Michelin map #303 (Calvados, Manche). These are a crucial resource for researching scenic drives and finding interesting towns/villages/sites to visit. The maps have nothing to do with using goole maps (or similar) to get driving directions from point A to point B (though you can use them for that in non-congested, rural areas). You want the ones of the scale 1:200,000 (regional maps) or 1:150,000 (departmental maps, more detailed, cover slightly less area) for whatever regions you visit. The Michelin maps have icons for all kinds of historically/touristically interesting things such as châteaux, ruins, churches, abbeys, scenic view points, caves, Roman sites, megaliths, designated scenic roads (highlighted in green) and many other things. A nice feature of the 1:150,000 maps is they show the starred attractions in the corresponding Michelin Green guidebooks.
You'll notice loads of designated scenic roads on the map in this region (highlighted in green) and they are all lovely. As a matter of fact, most of the roads in this area that aren't designated as scenic on the map are also lovely. Towns/villages you can consider stopping in to stroll around for a few minutes are Beuvron-en-Auge, Beaumont-en-Auge, Cambremer, Cormeilles, Blangy-le-Château etc.
A place I really enjoyed visiting in that area was the Domaine Saint-Hippolyte, a 16th century farm/manor you can visit where they are making/producing cheese and you can explore the grounds and buy all kinds of wonderful products from their shop, and have a picnic on the grounds if you'd like:
Do what you wish but if it were me then after leaving Rouen I would first visit Honfleur and then take advantage of the fact that I had a car and skip Deauville/Trouville and do a scenic drive through the Pays d'Auge region. For me, the best part about visiting/vacationing in France is getting off the beaten path and wandering around in my car on scenic country roads and passing through/stopping in anonymous country villages (where I often have encounters with the locals).
If you want suggestions on days 3 and 4 then maybe you could mention if you have to return to the car to Paris at the end of day 4 or what your plans are at the end of day 4 as that can influence advice given.