My question is could the flaps be lodged further down exhaust tube and clogging up exhaust? Maybe cause of all the problems?
They would wind up in the bottom of the Y pipe. They would restrict exhaust and water flow, and in most cases just reduce the amount of power because of the exhaust restriction. Have not found the restriction to also cause over heating manly, IMO if there is less HP there is less heat.
After a while the flappers can break up further and get expelled. Need to have a look and see if they are still there