Below is the proposed itinerary for the New England trip my husband and I are taking this fall. Our focus is to do outdoor activities – primarily hiking and biking – and some scenic drives. I need to do a bit more searching on Fodors for specific hikes and drives, but wanted to first get an idea of the general game plan. Is this enough time in each location, and have I selected my bases appropriately? And, generally speaking as I know Mother Nature will have the ultimate say, have I timed peak (or thereabouts) foliage correctly?

Oct 3 – Arrive in Jackson, NH. Hiking in afternoon
Oct 4 – Hiking/biking White Mtns
Oct 5 – Scenic drives in NH
Oct 6 – Hiking White Mtns
Oct 7 – Drive to Stowe, VT – scenic drives
Oct 8 – Hiking Green Mtns
Oct 9 – Scenic drives in VT
Oct 10 – Drive to Lenox, MA – scenic drives
Oct 11 – Hiking Berkshires
Oct 12 – Depart

Your timing should be great for peak foliage in the north. On your way to Stowe you could stop at the Great Vermont Corn Maze in Danville. It's very challenging and a lot of fun. But, personally, I wouldn't choose Stowe as a base for that time of year combined with scenic drives. The route from Waterbury is lined with shops and attractions such as Ben & Jerry's factory so I would expect a lot of traffic congestion. Not sure if there's many alternate route choices. I like a location further south. Even a drive to Burlington would be a long one. Maybe a hiker would have a good recommendation.
You can buy an Atlas and Gazetteer for each state. They are published by Delorme. They are oversized pages with detailed road maps plus the location of hiking trails, waterfalls, covered bridges, etc. They are really helpful if you like to drive off the beaten path and in northern VT that can include a lot of dirt roads.

Just wanted to top this, as I want to make reservations soon, and I'm hoping someone can give me a recommendation on where to stay if not Stowe. And is Lenox a good base for the Berkshires? Or should we stay more north? Thanks...

From Jackson to Stowe you can avoid Route 100 all together. Take Route 15 west from West Danville to Morrisville, where you can take Route 100 south. There are also ways around Route 100 south between Stowe & Waterbury (back roads that you can find on a Vermont atlas & gazeteer). IMO Stowe is a great destination as is Jackson and your other choice. Your timing sounds great, but as mentioned above, make your reservations now if you have not done so already!

Hiking sounds great. Be prepared to dress in layers for cold New England weather. This is especially true on the high peaks of NH where winter like storms can sneak up on you.

We live in Jackson most of the year, so if you need recomendations please let me know. Dinner, places to stay, hiking trails, etc.

We also go to Lenox every Labor Day week. Love the hiking and the town!!