Hello MH, I suspect, as you have observed, that there are bits/ chunks of rust circulating about the cylinder jackets and water tubes. The only thing I would suggest is blowing and flushing the cooling jackets AFTER you remove all the tubing AND the fittings from the cylinders. Air blow might be most effective with jacket passages completely dry (wear eye protection). As a last resort remove the core (“freeze”) plugs and repeat the cleaning.
Also, when removing the threaded fittings from the cylinder jacket closely observe how far into the colling passage the fitting extends. Sometimes the fitting will screw in so far that it comes very close to the inner cylinder wall severely restricting or blocking water flow. If this is found, shorten the threaded portion of the fitting.
Joe B
