Congratulations to your son! I hope he gets into all those smart people schools (or at least the ones you can afford). Also, both of you should read "Crazy U: One Dad's Crash Course in Getting His Kid Into College". Very funny and fast read that puts the college search experience in perspective.
Comments where I know something:
Rome: Good plan. Remember the Vatican can be pretty crowded. Consider a tour if you aren't going to be there long. A lot of the tours have special arrangements where they can go to the front of the line.
One day in Florence/Venice: You could easily spend two or three days in each, but if you are going to do one, hit the churches in both places. Climb to the top of the Duomo in Florence and take your camera for the view. Just go walking in Venice. Venice is very small so you should be able to walk all three bridges over the Grand Canal. See St. Mark's. I would skip the gondola ride. There are no cars on Venice so be warned.
Paris: The Louvre is the Louvre, but if the crowds are scaring you off (and it is really crowded), try the Musée d'Orsay. This is where all the artwork that you actually are familiar with is. Monet, Van Gogh, etc are here. It is my favorite museum in Paris. The Notre Dame is indeed a must, but if you have time to walk around that part of town, there are several other smaller churches that also feature the Gothic design. For food and cafes, stroll down the Avenue des Champs-Elysees.
Scotland: If you can make Sterling Castle, that is the one to go to. The Edinburgh Castle is nice and all, but Sterling is where the history was made. It is a real fortress that saw real battles and I don't think it was ever taken by force.