Check out Motorcycle Rental Italy – a site I stumbled upon while looking at motorcycle touring in Europe. They rent V-Stroms and BMW 650's, and rent motorcycles from Sicily, Rome, Pisa, Milan. Two weeks cost about $1400 Euros (with a $2500 deposit), which sounds quite reasonable to me. Check out their suggested routes. From Milan you can take off to Lake Como, the Italian, Swiss, and French Alps. From Sicily you can explore the island (and take the ferry to Sardenia (overnight) and the mainland to the Cinque Terre and all that. (Sicily is hot, by the way, so if you're staying in the south, plan for a late fall or early spring tour there.)
I love touring in Italy. Normally I get my bike at Moto Guzzi in Mandello del Lario, which I highly recommend. (Check their rates rates and routes. They will discount for longer trips, so just ask Alis, and tell her I sent you.) I haven't' had any direct recommendations for CIMT, but if anyone has, please let me know. I'd like a recommendtion for a rental place farther south.