What "rods" are you referring to? The valve stems maybe? If it's just surface rust, no big deal, just squirt wd-40 in each port, turn the motor over and do it again until you get it in all cylinders. Check to make sure that you do not have water in the cylinders. If I leave a motor exposed(open ports) for any length of time, I squirt a rag with wd40 and stuff it in each port. Pay attention to them throughout the winter, you might turn the motor over and relube it also, keep it dry.
as for your exhausts... check to see if they have any cracks anywhere, and what about the flappers on the back of the boat? Can't be a whole lot of help with the exhaust, all I run are headers. Someone in the know will pop-up and let you know......good luck
the dog