You can fill the water jackets with a weak phosphoric acid solution. Phosphoric attacks base metal much less than hydrochloric. Neutralize with baking soda and water. I have seen this done with a complete assembled 235 Chevy motor to clean up very dirty water passages. The motor was set vertically on the bell housing, the water pump removed, the thermostat housing capped off, and the water passages filled. After about a week, this was drained & rinsed out and the baking soda solution was poured in for another week. A final drain and rinse and the water passages looked very nice.