I did my water pumps and when testing I also had a problem with overheating alarm on one engine.
Flow looked good (same) on both engines. We did use a Y connector and put water to the ear muffs and to the flush port.
troubleshooting with thermometer gun found one side of engine too hot 190 vs 120. Checked tstat, it was open but didn't look wet.
Long story short, stuck the engine in an old dock box and filled 'er up.....ran like a charm...