Our daughter absolutely wants to see Paris so we're thinking three-ish
days there. We're not the type of people who need to see everything -
If we don't check off the main tourist sites were OK with that - just
trying to absorb the culture and vibe.
It sounds like you've got the right attitude to avoid making Paris merely a "checklist" visit. You may already be thinking along these lines, but with only three days, if you and your daughter do not really have any real personal need to see anything in the Louvre or similar major site, you could skip it (that could save you an entire afternoon) and instead check out some of the small, charming museums and churches that most people miss but have art just as good.
I just love walking around Paris, exploring everything on foot and often just discovering things as well as getting a sense of the city layout and neighborhoods from walking around it, and that sounds like a good fit if you're hikers.
I've been to Cinque Terre twice, but only way back when Rick Steves just started talking about it; back then it really was special. The thing about finding that kind of experience today is that there are A LOT of other scenic little cliff villages and hiking trails along the coast you could also explore that have similar charm and sea views, are not so jam packed with tourists, and where the lodgings are still owned by locals. Some are just a few miles north or south of the Cinque Terre.
our daughter wants beach time (although she gets that European beaches
are not the perfect Sandy beaches that she's used to from Hawaii.)
I've spent afternoons on a beach that was huge, sandy, and mostly empty on an island just outside Tavira, Portugal (yes, I heard of the place because of Rick). So maybe the Algarve is one place to look, although perhaps not in the most touristy towns.
One crazy thing Paris does in the summer is pour a lot of sand along a stretch of the Seine to make an urban beach (Paris Plages). But I think it starts in July. That would not be what you're looking for, it's just a curious and fun thing that they do.
Our son loves World War II history but not quite sure how to weave that in
Well of course you already know there's Normandy if it fits the itinerary. I do like that part of France. I have a similar fascination about WWII but not enough that I change my itinerary for it. It's more like I notice when a place I happen to be in has WWII significance because of a museum, memorial, or plaque in town. Based on that, here's one idea:
Once you start locking down your major destinations, have your son research what happened at or near those places in WWII. Given that you'll be in France, Italy, and maybe Greece, there's a pretty good chance something happened in WWII near wherever you're going to be, whether it's a battlefield, a former military installation or airfield that is now a museum with artifacts like vehicles and airplanes, a former artillery installation on a seaside cliff that now gives tours of their underground bunkers, etc.
Given that your family likes the outdoors, you could for example research and plan a day out in some semi-rural area that involves walking down scenic trails that pass a WWII site.
I just did a quick web search and apparently in Paris alone, there are more WWII museums and memorials than you can ever fit into a 3-day visit...