I don't really know dining in the Acadia area and haven't really heard many raves about anything there. I think the Camden/Rockland area has a lot more to offer as far as dining, with Primo, Francine Bistro, Waterman's Beach Lobster. And Portland is a great dining town.
So I think I'd say Camden/Rockland on the 1st night with a stay at High Tide Inn (moderate/rustic/former estate, a couple of miles out of Camden right on a cove) or maybe Camden Harbour Inn right downtown near dining.

Then two nights and most of the 3rd day exploring Acadia maybe at the Asticou Inn a few miles past bar harbor?

Then two nights in Portland , Hilton Inn downtown Waterfront near all the great Old Port Dining. Or, Kennebunkport would be the 2nd choice if you're looking more for a quiet, out-of-the-city type of experience...maybe Kennebunkport Inn with dinners at Mabel's and Pier 77....or even the 5 star White Barn Inn if that's the kind of thing you enjoy.

Portland is about a 2 hour drive back to Boston Logan Airport and Kennebunkport just over 90 minutes, so plan accordingly on departure day. A flight out around 3 or 4 pm is probably ideal and will keep you out of Boston Traffic.

You can find lots of recommendations on chowhound.com northern New England thread.
Keep in mind that some of the lobster shack places like Waterman's are either closed after Labor Day or open weekends only until Columbus Day. The Harpswell area (east of Brunswick)is lovely and rural. You might check Dolphin Bay Marina or Estes' restaurant. If you are really lucky, you'll find a community supper. We chanced on one to benefit a local volunteer fire dept a few years ago. Lobster with a side of steam mussels, etc but I'd go for a good ham and bean supper, too. This July we had a good chicken barbecue put on by the Rotary in Bath during their Heritage Days. I do have a special spot in my heart for Waterman's which we try to visit whenever we are in the area. I think the setting is part of the appeal. Great ocean view and no other commercial establishment around. I know locals eat there as well as tourists because on our first visit we eavesdropped on a man complaining about mowing the lawn for a summer owner.

If you are on Rt 1, check the open hours for Schutty's Seafood. It's just a truck parked by the side of the road in Bath, New Meadows road. They weren't open their advertised hours but when we did catch them open, they've got an interesting menu for a food truck. I believe they also source local ingredients. I enjoyed a crab roll with avocado and tomato.

On Rt 1 in Stockwell Springs, Just Barb's is still popular. We haven't eaten there in several years but still see it mentioned on chowhound.

Portland is considered the foodiest city in the US. The food tour is fun and interesting. Duckfat's french fries are really special. I don't think you should miss Portland just because it might be filled with tourists.

We also managed to go to 3 or 4 farmers markets while we vacationed this past July. The one in Bath was esp good. Great place to find a good pastry and perhaps a goat cheese spread for cocktail hour at your hotel. You can find a listing of markets by googling.

There are a number of good places in Bar Harbor, Our favorite is Cafe This Way, I can mention more later in the day.

~Liz

I posted some suggestions on your other thread. Want to second Duckfat for their great fries and they have good sandwiches. Also in Portland a very nice B&B is the Danforth. It's about a 10 minute stroll to the harbor. We have also stayed at Morrill Mansion which is also about 10 minute walk to the harbor.

In SWHarbor we had a nice dinner at Red Sky.

I love the Harpswell area, but with your limited time I would skip that area for this trip. Also we had a terrible meal at Dolphin Bay Marina - perhaps we hit an off day.

We stayed at Berry Manor Inn in Rockland and it's a very nice B&B. Had a nice dinner at Good Company, but if you want lobster, head out to Waterman's if it's open.

I cant leave out Red's in Wicassett. The debate goes on about it, but we go to Maine almost yearly and consistently have the best lobster rolls there. They can be a dollar or so more than some other places and u might have to wait in line 10 minutes or so, but I think its worth it, the lobster is fresh and sweet and u get alot on your roll. Also on Rte 1 outside Freeport, North of Portland, is a place called Cindy's that also has really good lobster rolls and clams.