There will be little or no change in the timetables between now and whenever you are travelling.
Advance payment is a waste of time for Florence-Pisa and for connections using Regional trains all the way to Santa Margherita, as there are no reserved seats and no advance reductions. Buy tickets for these trains in Italy, these tickets are OK for two months on any train until validated (time/date-stamped) just before boarding.
Tickets from Pisa to Santa Margherita on InterCity trains and Pisa to Rapallo on Frecciabianca trains can be booked now for dates much further away than June 9, though I haven't checked how far.
Edited: 18 May 2012, 11:27