When I restored my 66, I removed the engine and had it up on a stand for 5 years, just turning it over by hand once a week. When the car got reassembled, the fuel pump began to leak, and two weeks later, the water pump gave out (it was newly installed just one year before the engine was removed. Despite removing all of the coolant I could, there was still coolant in the block and the water pump was corroded where there was water. I believe the seals dried up, though, causing the failure.
I would recommend removing the water and fuel pump (along with whatever else has seals) from the engine, cleaning the guts and drying it out for long-term storage.