Okay, here we go!
You’ll be heading east on the Pike, so be careful — lots of big-rig trucks. If you’re at all historically-inclined, go to Sturbridge Village for a few hours and stop by the Publick House Inn for fabulous bakery foods and/or a cozy autumnal dinner.
When you reach Boston, stay inside the city to maximize your stay: it’s worth the cost and will remove some of the hassle and driving. I suggest the LongWharf Marriott for its centralized location — food, attractions, and waterfront all rolled into one. You’ll want to lunch in Quincy Market (cheap) and do dinner and dessert in the North End (splurge here, it’s well worth it). I think you’ll be happy enough with two nights in the city, considering you’ll be heading north next…
Salem is fun, no question. If you’re into museums and tired of witches, head over to the Peabody-Essex Museum for an afternoon. I don’t have any hotel recs for this area, unfortunately.
Your best bet for a decently authentic but not too expensive Maine experience is a combination if Portland and York/Ogunquit/Wells. Portland is a revamped but still active Port city with great shopping, nice harbor cruises, and seafood galore — for lobster or fried clams, go to the Portland Lobster Company right on the water. Stay in one of the many B&Bs that are located right in town, and enjoying this walkable city.
In York, you could stay at the York Harbor Inn, or choose from one of many, many hotels in Ogunquit. Go to Nubble Light (ahem, see my avatar!!) for romantic pictures, and go for a walk around the Rachel Carson preserve for foliage, wildlife, and woods. Or, walk the Marginal Way in Ogunquit to stay active seaside — while down at Perkins Cove (Ogt) grab some penny candy, check out the drawbridge, and eat at the Oarweed. For the most authentic lobster experience in southern Maine, go the the Lobster Pound, choose your own, and order some fall beer. You won’t be sorry.
I think a week is enough for this trip. I tried to keep in mind that it’s your honeymoon, so the drive times are limited and all are very Kodak-moment worthy. I have oodles of suggestions for spas, hotels that are anywhere from ** to *****, and restaurants for all occasions. But… I hope some of these suggestions help!