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You could actually use Rte 1 for a lot of your trip

I just came back from that part of Maine earlier this week. A friend of mine started out in Portland and drove as far as Bar Harbor where we stayed two nights. We toured through Acadia and went to several other towns in the vicinity (the other "harbors").

Next night was spent in Boothbay Harbor and then back to Portland. We used Rte 1 for a lot of the trip and stopped off in Camden, Bath, Brunswick, etc. Traffic was actually pretty light and that helped a great deal.

There are many variations on routes but this plan worked well for us.

http://www.fodors.com/search/results_community.html?search=Maine+September

It really depends on your interests. If historical, Salem MA for the Peabody Essex Museum and Portsmouth would make good stops for Strawbery Banke. Unless you want to hike the rocks, I would not go to Monhegan but would do another boat ride instead such as Portsmouth harbor or Portland's mailboat cruise. I don't think there is a Bath Maritime Museum lighthouse cruise scheduled during your visit but with a lot of googling you can find other cruises.

We prefer the mid-coast area so I would take I95 as much as possible, getting off in Brunswick for US Rt 1. It goes right thru downtown Camden. It can get to be a long ride north of Camden but you can take a faster route when you go south. Keep in mind Friday afternoon is going to be heavy traffic heading north. I would not visit Boothbay or Camden on a Saturday even after Labor Day.

If you are more interested in food and wine, I would take the food tour of Portland which will take most of the day. Between Portsmouth and Portland you can stop at Stonewall Kitchens and When Pigs Fly bread outlet for tastings and goodies. In the Camden area, visit Cellar Door Winery. Try to visit as many good lobster places as possible but be aware that after Labor Day, some of them will only be open weekends. Five Islands has probably the prettiest setting (these are outdoor picnic table type places). I like farmers markets. Some have ethnic food vendors that make great lunches.
If you are not planning on hiking or biking in Acadia, I would make it a day trip from someplace else i.e. Camden (still a long drive) to avoid changing hotels so often. If you stayed in the Wiscasset area, you can easily visit Camden, Bath, Brunswick, Boothbay, Rockland. If you do go to Acadia and are interested in history, consider a stop on the way back in Bangor at Cole Transportation Museum where you will see more about the logging industry than about lobsters.

I’ve had a chance to check out other posts and with the info here I’ve come up with a first pass itinerary. We are interested in visiting some quaint shops, restaurants, hiking, coastal areas, etc.
Thursday afternoon – drive to Portsmouth and spend first night here. (Hotel and Restaurant suggestions?)
Friday - Rt 1 to York, York Beach, Cape Neddick, Cape Elizabeth
Friday evening - Portland
Saturday morning – I95 to Bar Harbor, lunch, hike
Saturday evening – Bar Harbor
Sunday – Schoodic Pennisula or Blue Hill area, drive to Camden
Sunday/Monday (2nights) – Camden
Monday and Tuesday – Camden, Wiscasset, Booth bay, Bath
Tuesday evening - Brunswick or Portland
Wednesday – I95 to Boston with possible stop in Salem or Marblehead? Flight home is 5 p.m.
Is this a reasonable schedule? Will it allow time to enjoy without feeling rushed? I tried to plan around the high traffic times and keep driving time to a few hours each day.

I've never been to NE but I'm planning a trip in September just after your dates. We will only have 3 nights in Maine, and will be flying into Portland and staying in Lincolnville, just north of Camden.

I'm sure others will chime in if I'm off base here, but the 2 night stay in Camden is a little odd since all of the other locations you plan to visit on Monday and Tuesday are south of Camden. It might make more sense to base yourself just a little south of Camden so you are in between the destinations you plan to visit for those two days.

You've shortchanged the York/Ogunquit/Portsmouth area, but your real error is on Saturday. A 4 to 5 hour drive to Bar Harbor just to hike and then up and leave the following morning.

Better to head to Camden area on Saturday and settle in for 3 relaxing nights. You can do a nice day trip back and forth to Acadia on Monday. leaving early, stopping for breakfast along the way, and spending a full afternoon at Acadia/Bar Harbor. Stopping for dinner on the way back to Camden will make it an nice, easy drive. It's a nice drive anyway that time of year.

Tuesday I would head to Portland, a drive out to Cape Elizabeth/Two Lights Park for lunch and then hotel check-in. Late afternoon and evening to visit Old Port / Fort Williams Park etc. Wednesday you won't have to rush out of Portland but you do want to be at Logan airport around 3pm to return the rental car and avoid late afternoon traffic. From 10am to 11:30 you could drive down to Salem or Marblehead, have a shoreside lunch and look-see, then around 2pm head to the airport, maybe even down coastal route 1 instead of I-95.

That leaves you with two nights at the beginnning of your trip in Portsmouth or Ogunquit area. The York Harbor Inn is nice and you can easily visit Ogunquit, Portsmouth and York Village from here. As far as Boothbay, Wiscasset, Bath...well, you can't see it all in just 6 days. You can drive by and wave, but what's the point? You could do a Sunday afternoon drive to one of them if you really want to see it.