I would think that if your intent is touring you could do best with a combination of rail pass (for going from city to city) and car rental (for getting off the beaten track near your cities) and not worrying about flights.

Here's a good guide to rail passes (published by travel guy Rick Steves):
http://www.ricksteves.com/rail/railpdf.htm

I have to wonder how much additonal burden (luggage, Huggies, etc.) will be posed by traveling with a 9-month old. I've seen other train passengers with an infant and you have my respect for feeling up to pulling that off...