Clear it away
When you get back aboard, carefully clear away anything that might be damaged by an acid-solution spill. Clear your cushions and other stuff well away because this job can be a mess. Put the female garden-hose connector on the discharge hose and clamp the other end of the discharge hose to the cooling-water discharge stub by the exhaust manifold. Install and clamp one end of the double barb into the engine-water inlet hose. Connect one end of the hose from the drill pump to the double barb and clamp that connection.Finally, clamp the hose connections on the inlet and discharge sides of the drill pump.

When you're done clamping, you should have hoses leading from the bucket that will contain the clean acid solution to the drill pump to the cooling-water inlet. The other hose runs from the cooling-water discharge to the waste bucket. Charge your dock hose with fresh water and keep that water source running and ready just in case you have an acid spill. Re-secure the thermostat housing cover before you start pumping the acid.
  Mix the acid
After all connections are clamped, you are ready to mix the acid solution. Put on your safety glasses and fill one bucket with about 5 gallons of fresh water. Slowly and carefully pour 1/3 gallon of muriatic acid into the water. This is the proportion recommended by Don Moyer. (Caution: the chemistry prof says always pour acid into water

  -never, never pour water into acid. When you pour water into concentrated acid, it can "explode" and get the acid all over you. -Ed.) Start your drill pump and let the acid solution pass through the engine block until the clean acid bucket is about empty. Then stop and wait 15 minutes as the acid solution in the engine block dissolves the rust and mineral deposits.

You can use this interim period to remove the dirty acid that has passed from the engine to your discharge bucket. Rinse both buckets, filling one with clean fresh water. Before you dispose of the dirty diluted acid/water mixture, be a good guy and mix it with common household baking soda at the rate of 1/2 pound of baking soda to 5 gallons of water. It is going to foam when you do that, so put it in a little at a time and don't put your face or other skin parts over the liquid while you are neutralizing the dirty acid.

After 15 minutes, flush the block with fresh water using the drill pump, with the acid and crud passing from
  the block to the empty discharge bucket. Empty the dirty bucket and refill the clean bucket again with fresh water and repeat the freshwater flush.

Now hook up your dock hose to the female garden-hose fitting on the discharge hose and disconnect the drill pump from the inlet line. Back-flush the engine with fresh water moving backward through the engine under hose pressure as even more crud is discharged from the inlet hose to the buckets.

After removing about 20 gallons of back­flushed fresh water and crud, disconnect your flushing hoses and reconnect the usual engine­cooling water hoses. Start your engine and see if you didn't knock about 25'F off your engine's operating temperature. If you've a manual thermostat, just dial in whatever operating temperature you like.