This should be an unforgettable vacation. You could not have chosen a better destination, nor chosen a better time of year. I was born here (in Vermont), lived here all my life, have done a fair amount of travelling, both here and abroad, but I thank God everyday that he planted me here. Autumn is my favorite time of year. I spend the rest of the year looking forward to it. There is nowhere else on earth I'd rather be in October. We do get lots of visitors this time of year (I love to look for the out-of-state license plates when I am out peeping at leaves--they always outnumber the Vermont plates), but I have never been caught in a traffic jam because of them so this shouldn't be a concern to you.

Having grown up in Burlington and currently living in an adjoining city, I have a bias towards it. I think you need to stay at least one night in Burlington or you will regret it. There is much to do here and many excellent restaurants especially for a city of its size. The Marketplace is vibrant and fun and located only a few blocks from Lake Champlain. You can take a cruise on the lake, ride the ferry or just walk on the boardwalk. Whatever you do you will have a wonderful vista in front of you--the beauty of the lake is exceptional with the Adirondack Mountains of New York as a backdrop
--just spectacular, especially if its a clear day and the mountains are at peak color. It's a great place to see some beautiful sunsets. I think they are better at this time of year--might just be me, but the colors seem more intense.

You mentioned covered bridges. You can find them in several places in Vermont, but of the places you have mentioned, you will find one near/at Shelburne Museum, one in Middlebury as you head towards the UVM Morgan Horse Farm (you will have to drive over it), and another in Woodstock. This is a quaint but wealthy town, with wonderful architecture--very picturesque. It's not far from Quechee which has a rather impressive gorge. As I recall there is a huge antique store in Quechee or just before if that is your interest. Anyway, Woodstock and Middlebury (and also the Manchester area--and Stowe, of course, is a given), are my favorite destinations when I am leaf-peeping. Oh, in Middlebury, a restaurant you might enjoy is "Fire and Ice". I have always found it to be very good and not too pricey. A less expensive but very good choice (and probably the only one that isn't fast food) for a late night dinner/snack is "Mr. Up"s". It seemed to be quite popular with the college crowd (there was entertainment) but also seemed to attract many who were well beyond their college days.

Anyway, hope you have a great time in New England. I'm sure the Vermont portion won't disappoint.