I would highly recommend making a reservation for the Vatican Museum. Go to http://mv.vatican.va/3_EN/pages/MV_Home.html to buy your tickets online. You can pay for them now and print the tickets to take with you. Having a reserved time and prepaid ticket will cut your waiting in line time from 3+ hours to maybe 15 minutes. Also, you cannot wear anything sleeveless, too slutty or casual at the Vatican. Khakis, dresses, sweater sets, etc. are fine. Jeans are ok, too – just not short shorts. I would also recommend bringing addresses of people you’d like to send a postcard to (including yourself) and buy some postcards at the gift shop. The Vatican has its own post office with its own special Vatican stamp so it’s kind of cool to get a postcard from the Vatican.
Also, I highly recommend the Roma Pass. You can get it at the main train station (tourism office) or airport. It is valid for 3 days from the time of “activation” and gets you into two museums for free, other museums at a discount, and unlimited trips on buses and metros. It's about $25 EU (about cost of two museum entrances) and you get the ease of being able to hop on and off a bus or metro anytime even for just one stop without having to buy a ticket every time. Keep in mind the metro part of the card and the museum part are completely separate systems and each have their own "clock" that starts at first use (valid for 72 hours). Additionally, the Roma Pass comes with a good map of Rome and a booklet that gives you a description of each museum, their hours, cost, and major sights. The best part is you could call the customer service number and ask the English-speaking attendant anything like "I'm trying to go from to . What's the best way to get there?" and they'll tell you exactly what bus/metro to take.
I have detailed tips covering transportation, accommodations, museums, shopping, etc. that I can send you if you'd like - just email me!