I'll throw out some thoughts.
It would help to know what cylinders fail when it goes down to 4 cylinders.
Systems are paired. On the ignition side 1&6, 2&5 and 3&4 are the combinations. So if one of these combinations dies, it could be a coil, or a Darlington transistor in the igniter, or a pulse coil that fails when hot,, or a fouled spark plug ( since in a wasted spark system, the spark travels down one plug wire, then across the sparkplug gap, then through the engine cylinder head /block to the second plug, then across the gap and back up the second wire to the coil to complete the circuit.
Then on the fuel side we have pairs. 1&2, 3&4 and 5&6 but only the float bowl /fuel supply is common. As far as idle circuit, Main circuit, choke circuit, they are literally individual carbs. The throttle barrels are operated together.
so you mentioned that 5/6 may have gone down together. Could be a fuel flow problem to the 5/6 carb??
The pulse coils operate at 5-8 volts and trigger the Darlington transistors in the igniter. With such a low voltage and low amperage any resistance in the circuit between the pulser coil and the igniter could be problematic. Don't over look the connection between the plug connector pins and the wires themselves.
hope this helps, Keep us informed with what you find and we'll take it from there.
KB