A few comments:
1) Any chance you can spend more than 1 day in Florence? It was one of my favorite stops when I was in Italy and just one day really doesn't do it justice at all. I recommend at least 2 full days (I spent 3 but could have spent 5).
2) When I went to the Vatican Museum in March, it was a mob-scene. It's pretty much a conveyor belt to the Sistine Chapel. Seriously, it was insane. Unless you have a strong interest in art (not just that you like art museums) I wouldn't waste the money on a tour. However, I WOULD get reservations in advance since the line is ridiculous. When I went, I strolled right in with my reservation. I can't emphasize how important it is to have reservations for everything. It's usually 5 euro more a ticket and when you're spending hundreds, if not thousands of dollars on your vacation anyway, it's nice to not waste your day waiting on line.
3) My wife and I really liked the Borghese. Spring for the audio tour - it's great. The park is nice too. I went running in it each morning I was in Rome.
4) Instead of Pompeii, I urge you to consider Ostia Antica. We toyed with the idea of going to Pompeii as well but decided the transportation there would be too long and the area full of tourists and tourist traps. Ostia is an ancient port town that has great ruins, is so easily accessible by the subway system (about 30 mins each way), and will have FAR fewer tourists than Pompeii. It also has a great cafeteria (believe me, I'm a stickler when it comes to food) that is underpriced, if anything. If you purchase a Roma Pass (which I suggest you do), you can use your free entries for the Colosseum and Borghese, get a discount at Ostia, and ride the trains - this will cover the money you spent on the Pass. Also, be sure to stop at the Pyramid and Trastavere on your way back!