I did the VFR tour in May 2007 and had a great time. I got to Venice one day early and went to Padova (Scrovegni Chapel) the next morning, before the tour commenced. I would have like another day in Venice in order to see Murano and Burano.
Another couple of nights in Rome would be nice if only to accommodate a trip to Pompeii and Ostia Antica.
As it was, we left Rome on the last day of the tour and went to Bagnoregio for one night (best B&B I've ever stayed at), two nights in Siena and then two nights in Vernazza. Took train from Vernazza to Firenze where we caught plane to Frankfurt.
Though we had a car between the pick up at FCO and Siena, I would not do that again. Too much hassle to have a car anywhere near a city.