Planning a New England trip! Is this timeline doable?

I've lived in the exact area you are talking about for 30+ years.

You should check with the Maine tourism website frequently as right now they are expecting all out of state visitors to quarantine for 14 days upon entering the state.  https://www.mainetourism.com/travel-resources-covi... The lodging facilities are expected to police this AND you may need to bring proof (less that 72 hours old) that you are COVID free.   Maine in particular is overboard crazy regarding this COVID stuff, they aren't making it easy to be a tourist.  The tourism business is down due to this.  If you want to stay at a particular lodge/B&B/hotel I would suggest you call and find out availability.1 hour 20 min from Boston (depending on where in Boston) to Ogunquit is extremely optimistic.  

Beachfire Bar and Grill wouldn't be a place high my list of recommended restaurants for the area.  Beachfire is right on US Rt1, their fire pit is like 25ish feet from the road.    US Rt 1 is the main way in/out of Oqunquit, so it's busy.  There is a place in Ogunquit called Barnacle Billies that would be very similar to Billy's Chowder house in Wells, but fancier.  Barnacle Billies is right on the water (Perkins Cove) fantastic view.  Billy's Chowder House is on what we call the marsh, not as scenic and if you eat outside the mosquitos and no-see-ums can be a downer.  There are many many good restaurants in Ogunquit, without knowing your budget, food tastes etc.. it's hard to make a suggestion.

Wells is a place I've always driven through......never stop except for the Maine Diner on Rt 1.

Instead of Well's, I'd suggest you drive 15ish minutes further to Kennebunkport, ME. Much more to see, 1000x more quaint and what most people think of when they think the coast of Maine.  Just after the Maine Diner, take a right onto State Rt 9.  This will take straight into Kport.  There are lots of great restaurants in Kport, but on the bridge is a clam shack, it would be a good place for fried clams or a lobster roll, just be aware they serve their lobster roll on a hamburger bun, not the quintessential split top bun that other places use.  But, you do get more lobster on these than you find other places.  There is another "clam shack" we really like in Cape Porpoise, which is technically part of Kennebunkport.  It's called Cape Pier Chowder House, the setting couldn't be more picturesque.  https://www.capepierchowderhouse.com/

For recommendations on the way to Freeport I'd suggest you stop in Portland and find the area known as the Old Port.  There are ton of great restaurants in the Old Port.  Personal favorite is Eventide Oyster Bar (better like oysters) also Street and Company.   Portland to Freeport is roughly a 30 minute drive.  You have to drive right past Portland to get to Freeport.   

You mentioned adding a day in some of your responses.  If that's possible, I think it's a good idea.

Where are you driving from?  I live about a 4.5 hour drive from Boston according to any travel site or map, and go back there frequently (Boston was original home.)  It usually takes me 6 hours, especially on a weekend.  If you are coming from south of New England and will be taking 95 through CT, tack on an extra hour to your estimate.  You may also want to look at alternatives to that route, but still add on extra time.

It sounds like you planned a partial day in Boston.  You won't be able to see very much, especially if you're planning to be in Ogunquit for dinner (that hour and 20 seems like a low estimate on a weekend afternoon.)  I would recommend spending the entire day in town.  Enjoy dinner in the North End.  Spend the night.  Head to Maine on Sunday morning- if you leave early, you won't have much traffic.

This part of Maine is not within my expertise (I vacation all the way north), so I won't weigh in on that.  As someone else already mentioned, keep up to date with quarantine and testing requirements, which change depending on where you're coming from.

Oh, and have fun!  I think you've planned a lovely trip- even though it involves quite a bit of driving, it seems like your Maine days can still be somewhat relaxed.

Very ambitious plan.Since Maine is busy during the summer and fall, make hotel reservations at the hotels you want to stay. Have fun.

You're not giving yourself a lot of downtime between driving - did you want to relax, or are you happy spending lots of time travelling? 

No idea where you got travel times from, but during vacations season, and weekends in Sep still count. That drive Sat night from Boston to Ogunquit is gong to be more like 2 hours. That 15 min drive to Wells, will be more like 30.

Personally I do not think it is enough time to explore properly, especially anything besides the tourist traps. But is sounds like a decent enough trip.