Yes battery stuff is very confusing, especially volts.
The only time that volts give any indication of state of charge is when batteries have been standing without charge or discharge for several hours. Then about 25.2v indicates full charge.
If there is any charging at all then volts will be higher. If any discharge is taking place then volts will be lower.
If you are furling at about 40A then the C40 will be fine, but choose a dump load that will not exceed 40A. If you have a very windy day and you have an average of over 40A coming in and volts start to rise then you can switch a bit of load on.
State of charge of the battery is not going to significantly affect stator heating, the alternator doesn't know if it is boiling a battery or heating a heater. Heating in the stator will be determined by alternator design (resistance) and maximum current at furling.
Your batteries will take 40A when in low state of charge so you need not set furling lower than needed for safe temperature. More batteries will indeed let you charge at higher current to a higher state of charge and will also let you use more load for the same depth of discharge. More is better up to the point where you can no longer fully charge in a sensible time. In the extreme case of too much capacity you will not be able to supply the current to get them up to gassing volts except at infrequent intervals. This will require constant equalising from another source (inverter in your case). If you get good winds and you want to make better use then doubling capacity would make sense.
I doubt that you have done any damage to the batteries, but get the sg up as soon as possible and monitor it. If you have significant periods of low wind and sg falls, use the inverter to bring sg to at least half charge if you think there will be wind soon. If the wind doesn't come in a few days use the inverter some more.
Flux