Your electrical current needs while bike is running are provided by charging system and not battery. Battery is storage for starting and is getting replenished by charging system. Now if your battery is in bad shape it will put extra demand on charging system and over time cause premature failure.
Don't forget that the battery in most motorcycles also acts as a source of power and a "voltage stop" at low RPM because the output of the charging system drops at idle. If the stator isn't generating a full 12 volts then the voltage of the entire electrical system is the higher of what either the stator or the battery is making at that point.
So low battery voltage at idle could cause spark issues if the battery's resting voltage is low enough
and the stator is not generating enough voltage to properly power the coils. Though in that case the battery would test low on the bench too with a multimeter, probably under 10 volts, and at idle the bike would test with abnormally low system voltage.
You are right in this context for DOHC CB750's but not all motorcycles are wired quite the same. For example my recently-acquired 1986 Yamaha XT350, which has a separate coil wound in the stator just for providing AC voltage for the headlight and taillight while running, can run perfectly well with a big fat capacitor in place of the battery because it has no electric starter and will run on a completely dead battery.
To reiterate one of my statements, the power being demanded by the vehicle is passed from the generator through the battery to the vehicle.
And on that note, I put a new battery in it and the voltage never dropped below 12.25V at idle. When the rotor comes in next week, I'll throw that in and see what happens to the charging system numbers.
Thanks, all.
Double-check the wiring diagram for your bike. I just looked at my 1980 and the output from the regulator/rectifier doesn't flow power only through the battery. There are two separate positive voltage outputs and one ground. The red/white positive voltage output goes to the starter relay to charge the battery, but the second is black and goes directly to the ignition switch, kill switch, starter switch, and fusebox as their primary source of voltage. All the lights, while your CB750 is running, are powered directly by the stator and not the battery!
Your "never dropped below 12.25v at idle" is a sign of that brand-new battery bumping up the whole electrical system with plenty of juice, but that doesn't tell you what your stator is putting out.
A misfire when fully warmed up usually makes me think ignition coils are on their way out. Physically inspect the casings of the coils. The bike dying every time you pull a plug cap regardless of which one is not normal -- usually a CB750 will run on 3 cylinders.