Hi Colin
You should get some information in the DIY Shore Excursions - Med Area sticky topic at the top of the forum which you can access
HERE. It has info on doing Rome DIY and I think Pisa may be mentioned.
We have done both and they were very easy and cheap. Pisa is only about 15 mins on the train. If you decide to go to Florence be aware that you usually have to change trains in Pisa adn the announcements are obviously in Italian! We only realised when everyone else decided to get off.
luci