My first trip to Rome my partner had set up a tour with ScalaReale. They've now changed their name to "Context".

http://rome.contexttravel.com/main/home/
I don't know how they'd work out the transportation as we met our guides at designated places and times.

Here's the review I put on my website:

If you've seen the sites of Rome, you've also seen the crowds of tourists scrambling after tour guides - each waving their tell-tale "follow me" signs - the yellow umbrella, the blue and white flag, the walking stick with the colorful scarf tied on. These all fall under the category of "how NOT to see Rome". A much better alternative is Scala Reale. This group offers a bevy of personalized tours (most maxing out with six participants). On our first trip to Rome we signed up for one of Scala Reale's tours and enjoyed it so much, we took two more in the days to follow. What makes them so unique? It's their guides. Most of them are American's studying or living abroad. Imagine if you will, taking their Vatican tour guided by an Art History major. Or being shown the sites of the Forum and Colliseum through the eyes of an architect. On each of our tours our small groups took well needed breaks at such places as a wine bar, a gelateria, and a lemonade stand. Each tour made for a memorable information filled half day. And in such small groups, I felt entirely comfortable asking as many questions as came to mind.