Ok, I would take a train from Milano Centrale to Florence (Firenze S.M. Novella) on the 29th. Sightsee and stay overnight. I would spend the $$ on a faster versus slower train to maximize your time: daylight is short this time of year.
On the 30th, do some more sightseeing in the morning and then take a train to Pisa Centrale. Stow your bags at the station and spend a couple of hours. Jump back on the train to Riomaggiore or Monterosso in the Cinque Terre: spend the balance of the day (again, daylight will be short!) and stay overnight.
On the 31st, do some more exploring and catch a late afternoon train back to Milan.
Explore train schedules/tickets here:
http://www.trenitalia.com/tcom-en
Oh, and look at tickets prices from Milan to Florence on Italotreno too: they often have some good deals:
http://www.italotreno.it/en
You do not have to order tickets in advance but you can land some very low prices by doing so. The risk you take is that the lowest-priced tickets are not refundable so if you miss your train, you have to purchase another ticket.