A quick update finally tracked down what was causing the 56 codes. The phone support guy told me to check the flow sensors to ensure they are spinning freely. They were just fine.
Then he had me take out the flow control valve at the very top of the heater attached to the outlet of the heat exchanger. After I took it out he told me to take the valve apart and ensure nothing was jamming the valve. So I took it apart and carefully removed all the pieces, and found no debris or lime in the valve, put it back together and called him with my findings. So now he was stumped... So 3 months later they finally send a Noritz Tech out to help me trouble shoot.
Eric from Noritz comes out picks a heater, and disconnects it from the multi system controller. Then he closes the hot water outlet service valve, and opens the T&P valve it flowed water for 45 seconds and then went to a trickle. He is like AH-HA the heat exchanger is either clogged or the flow control valve is clogged.
I asked him why there was water flow at first. He said that is due to the main flow control valve being closed and the bypass valve being open. After the water flows for a little bit the circuit board sends a single to the bypass flow control valve to close and one to the main flow control valve to open.
So he drains the heater down and takes out the main flow control valve. He ensures it is in the open mode and tries to blow through it, and cannot. So he says it is clogged solid. He then takes it apart, removing the servo motor, then unscrewing the top plate of the valve which the spring pushes up as he unscrews it. Due to the spring pushing up he had a puzzled look on his face. He then pulls all the inner parts out and say wow I never seen this before. Normally the spring and all these parts are one unit like a cartridge. But this one is broke and that’s why the valve was not opening properly. He went to his car grabbed a new valve put it in the heater, turned it on and it works perfectly now.
The trouble was the phone tech did not tell me the parts where supposed to be like a cartridge, and all in one piece. Go figure. Eric called the tech support guy I was dealing with, had a few words with him and proceeded to order me up new servo flow control valves for the other heaters.