It was my understanding (mostly from what I've read in books on the GD's instruments and I don't know how accurate any of it is) that Phil initially played an EB-0, then moved to a Fender, then version 1 of the Guild Starfire, after which he switched to the heavily modified Gibson EB3. Eventually, he lost or had the EB-3 stolen and subsequently played the Godfather.
But then again, I'm not a GD historian like some of the people out there so, I could be wrong as to some or all of these accounts.