First - using a syringe remove all the antifreeze from the reservoir container that is in the port lazzarette and disconnect the hose. Remove and clean the container.
Yes - remove the plug on the port side of the engine block and remove the filler cap. I cut a plastic bottle in half and directed the coolant into a plastic tub.
To rinse the engine and HX -  I poured one gallon of distilled water into the filler cap and let it drain from the plug below.
To flush the entire content of the the hot water heater coil I disconnected both hoses near the thermostat and I used a dinghy foot pump and forced air into the hot water heater hose and drained from the other hose.
You need 2 gallons of antifreeze, it must be suitable for diesel engine. Here is what I used.
2 Gal Antifreeze  Preston DEX-COOL Extended Life - with Ethalyne Glycol (EG) - suitable for diesel engines  Walmart # 001024731 $14.27
I was replacing all the engine fresh water hoses so by disconnecting the "L" shaped hose below the thermostat all the water drained.
Now putting it back together:
I used a funnel to fill the hot water heater coil with distilled water ( antifreeze's low viscosity made it difficult to pour into the small opening of the funnel ) and sucked the air out using the pump until water came out from the other hose - then I reconnected to the thermostat housing. Then I filled the engine block with antifreeze until it displaced the distilled water and antifreeze came out of the engine block. I placed pipe paste on the threading of the engine plug and reinstall plug.Then I filled more from the engine filler cap until it could not be filled. Then I placed the filler cap on.
At this point there is plenty of air trapped inside the engine block that must be burped. Fill the reservoir with antifreeze and turn on the engine and watch the water temperature. Turn off the engine quickly as the temperature goes above 160F. Loosen the water temp sending unit until you see bubbles coming out followed by liquid antifeeze. Be sure that you have plenty of antifreeze in the reservoir above. Tighten the sending unit until there is no more leaking of liquid.
There always will be some air trapped making the liquid in the reservoir go up and down as the engine cools and heats up. On mine the rise and fall is about 1/2" on the reservoir.
Next day after the engine has cooled and most of the antifreeze has been sucked into the engine from the reservoir - add more in the reservoir and repeat the engine temperature test. Do not assume anything - run the engine at 2000 RPM to make sure it is burped well.
Good luck - let us know how it went and take photos.
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