Water got inside of intake port where the piston rod is after i took intake manifold off. 5.8l 351w?
Old Man Dirt
Under the intake manifold on a Windsor block you find the valve lifters and push rods. The oil flow path for the lifters is up through the lifters, up the push rods (some leaks out in the valley as it is called) and down over the rocker arms and from there to lubricate the valve stems. So that oil is nothing to worry about! A small amount of water can be absorbed by the oils emulsifiers. Much of it evaporates off (or out of the oil) when the engine is at operating temperature. If you are worried about water in the oil- change the oil before operation. While you know how much water you saw get into the engine, there might have been more. If there is it is right at the bottom of the oil pan where the oil pump will pick it up first, which can be catastrophic. I would suggest changing the oil before you start the engine.
FlagMichael
I think the rod you are seeing through the intake port is the stem of a valve. If the water is reasonably clean there should be no harm... lots of oil there to protect things against water. Once the engine runs the water will boil off pretty quickly.
Pilsner Man
I really can't help, your description isn't very good. The piston connecting rod is inside the engine.