Hi again, Chris,
Given the amount of time which you have, three days in Edinburgh may be enough to take in some of the primary sights. However, as you said that you love small villages and quaint pubs, you won't find that in Edinburgh. Auld Reekie is the number one tourist destination in Scotland, and is crowded year round. If you do decide to spend some time there, you should choose ahead of time what you want to see, and plan your visit accordingly.
As most flights from the U.S. arrive early in the day, your plans should be determined by whether or not you can sleep on a plane. If you arrive knackered, best thing to do is to leave your luggage at your lodging, do some sightseeing, then have a light supper and get to bed early. (I'm speaking from personal experience!) That way, you can start out your first full day reasonably refreshed. (I feel as though I'm preaching to the choir here!)
You'll find that Glasgow is not as tourist oriented as Edinburgh. It's a fun city to visit, but the attractions are more far flung from the city centre than they are in Edinburgh. Trains and buses run pretty much hourly between the two cities. Travel time is pretty close to an hour each way. Try to find a good hand held map of the central areas of both cities. Public transportation is plentiful in both cities, and taxis are everywhere.
If possible, try for at least twelve nights, rather than ten. That way, you can expand the radius of your travel area.
Visits to Scotland are like eating potato chips (American reference from an advertising campaign) - you can't have just one!
Happy travels!
Mike (Auchterless)
p.s.: If I had to choose just one small village to visit in Scotland, it would be Plockton, on Loch Carron. However, there are dozens of others, just as deserving.
