If you take the inlet off without dropping the water first you will end up with water in the ports.
As said the inlet has water going through it to register temp on the sensor at the back.
So chances are you have filled a port with water. If the valve is open it will be in the bore and running down the side of the piston into the sump.
remove spark plugs and fuel pump relay. Turn engine over untill you have spat out as much water as possible.