I use a wire wheel for anything like this. I keep one on one side of my bench grinder. It removes the rust and burnishes the part's surface.
one thing, if a wire brush is used to clean off the rust, make sure that you run it length wise along the rod to minimize any stress riser formation that will weaken the rod.

So if I would fog the inside of the engine with the rotating assembly installed using ospho would it do any harm? Sorry I forgot to mention the rotating assembly was installed.
Don't know what you mean by "ospho" but if it's any kind of chemical stripper/cleaner.....................NO !!! Leave the rods as is and give em a good coating of motor oil.