Yeah, I'm not a big fan of the chain coffee places either. I don't really have any suggestions, though. I just get coffee wherever I end up eating breakfast.
Never spent any time in Manzanita, other than passing through. Pacific City is one of the places where you can drive on the beach, depending on what your rental car is. Pelican Pub & Brewery in Pacific City has great beer, and their beer battered fish and chips (made with their cream ale) is fantastic. Another good place for fish is J's Fish and Chips in Lincoln City. It's nothing special, just a little shack, really. But they have great fish. The Wifey and I eat there whenever we're passing through.
On your way to Newport, I recommend stopping in Depoe Bay. Lots of little touristy shops there, but there is a pod of grey whales that live there year-round. If you have the time, I highly suggest taking a whale watching cruise. You go out for an hour or an hour and a half, and they'll get you right up next to them a lot of the time. The whales being resident, are used to people and boats and don't get spooked. You can get some really cool photos. If you go, I recommend Dockside Charters. We went with them last time and liked them a lot.
In Agate Beach, at the intersection where you turn off to go to Yaquina Head lighthouse, there was a small cafe that we had breakfast at a few times and enjoyed. Last time we were in the area, they were closed and the building was up for sale. But if someone else has opened up a new place, it might be worth checking out. In Newport, you can go down to the harbor and get some shots of all the boats moored there, the bridge, etc. All kind of postcard type stuff, but still makes for some nice shots. You can also go out onto the jetties and get shots of the boats coming and going.
Something I just remembered: between Newport and Florence is a place called Thor's Well ( 44° 16.710'N, 124° 6.806'W). I've not been there yet, but it's on my trophy shot list. If you stop there, you'll want to be very careful. The best shots of it are at high tide, and apparently you'll need to be down on the rocks. Sneaker waves are no joke. They'll ruin your day in a big way.
I'm not familiar with anything in Florence. I've only been to the Dunes a couple of times, and never spent any time in town beyond driving through. If you decide to go further south, you might check out Sunset Bay. It's a state park and campground near Coos Bay, and is where my love of the Oregon coast first developed. It was my first trip to the coast when I was 11 or 12. If you have the time to stay a day or two, there are a lot of trails, botanical gardens, and cool rock formations. Plenty of great photo opportunities. Especially, of course, at sunset.
