I think I understand your desired direction.
1) You want to Fresh water flush your engine raw water cooling system.
2) You think Aluminum might be better than zinc in fresh water.
There is NO unexpected corrosion from Aluminum/Zinc anode mix, on the metals they are intended to protect!
Mix away!!!
Probably this is unwanted advice (my boat is about same specs as your)...
I wouldn't flush the sea water system with fresh water unless your down time would allow barnacle growth. Flushing will have negligible effects on galvanic corrosion and would probably increase overall corrosion by the dissolved Chlorine gas used for municipal water treatment. Chlorine loves to attack Aluminum.
Check the electrical continuity between each of your exchanger, after cooler and engine. Use a volt meter in Ohms mode. If they all show low resistance of say less than 10 ohms, your shaft zinc does them all. If not, then that explains the separated anodes (they wouldn't significantly effect each other in this case).
Lastly...
Pacification of Anodes.
From a reputable source.... NOPE!
Pure zinc and pure aluminum and pure steel (all pure metals), pacify themselves sitting around in open air.
The do NOT pacify when exposed in water to galvanic (electrical type) corrosion.
I have heard of many on this forum who clean and polish their zincs.

Why? Shrugs.
I recently opened and inspected my engine exhaust riser (14 yr old cast iron). It had no wear and had iron corrosion. My helper reached for a wire brush to clean the inside.
STOP! Don't clean off the protective barrier from sea water and acidic exhaust gases. THAT IS NOT GALVANIC CORROSION! I was protected from galvanic corrosion by my shaft zinc.
Jim...