Water in cylinder, now rust, now what?

Update. OK, I bought a fine wire wheel for my drill, but a neighbor handed me some 150 grit sandpaper to try first. The 150 grit took the rust stains right off! Returned the wire wheel attachment for a refund. I am not going to pull the pistons, but I did purchase a new timing chain because the old stock type was hanging. Hardly any ring ridge in the top of the cylinders for some reason. Used compressed air to clean out the cylinders and wiped 'em down with ATF before it began to rain and had to call it a day.