[Fr. Frank]

First pull the heads and clean as much of the water jacket as possible by hand, using phosphor-bronze bore brushes made for cleaning handguns. Clean as much of the water jacket on the block as you can with the brushes, too. Blow compressed air up through the pickup tube above the impeller housing, blowing out as much dust and corrosion as possible.
Reassemble the heads onto the block, using fresh gaskets, and re-torque to spec.
Run the motor in a tank made from 1/3 or 1/2 of a plastic fertilizer drum. Fill the tank with about 20 gallons of water and add 1 gallon of muriatic acid.
Run the motor in the tank with the diluted acid for about 15-20 minutes after the thermostats open.

You can also pull the thermostats, and then tilt the motor fully up to a trailering position, and pour undiluted pool-use muriatic acid right into the water passages on the heads, and let it run out the bottom. Sometimes you need to to this first, and then run the motor in the diluted tank.

BTW, DO NOT try this last trick with any outboard with a blind bore, like early inline 4 and 6 cylinder Mercs.