I've done some rides from Boston to Nashua, NH on a route similar to your day 12 plan. If you want a bit more scenery and history, go through Concord and take Lexington Road and Rte 2A to Lexington along the Minuteman National Historic Park. Sure, that's a couple miles longer, but it's quieter than the Great Road from Bedford, and considerably more scenic.

You could either take Route 62 (Concord road) from Bedford or Concord St from Carlisle (becomes Lowell Rd). There is a bridge under repairs, so Lowell road is currently the only way to cross the river by car in Concord. If you run into traffic, you can take your bike through the Old North Bridge park, where the battle of Concord took place.

The whole area is very popular with local cyclists and you'll probably see a lot of us out there with you!