A cooling system in otherwise perfect condition but with thermostat removed, and filled with straight water... should boil over until doomsday. Study, don't panic. I recommend pressure testing the cooling system with a tool for that. A cranking pressure test might help determine if a head gasket is involved. Monitoring engine vacuum might help determine if an intake manifold leak is present. If you found the system empty... was it cold and was that at the thermostat housing or radiator cap? Did you check the oil dipstick as mentioned earlier?
