Hi Tim,
Welcome to the ItaliaPass community and thanks for your question!
Really the only thing to be aware of regarding the Jubilee Year is that larger crowds are expected. With that in mind, I don't think you need to make any actual modifications to your itinerary. The city has taken measures to increase services such as public transport, and large infrastructure projects for better traffic viability have been underway for some time to help facilitate the increase in visitors. Personally I don't think it would be worth it to fly into Florence or Bologna. That would just add time and hassle to your trip. Rome's airport is consistently voted the top in Europe and there are plenty of easy connections into the city. The Leonardo Express train departs every 15 minutes and there will also be an increased number of taxis to handle Jubilee visitors.
Let me know if you have any other questions!