Technically a lead acid battery is considered dead if the voltage is below 10 V. At 1V there is probably damage to the plates. You may want to do a search for lead acid battery conditions and voltages. There are charts available that describe the condition for each voltage level.
I will try to go through the spreadsheet, but can't make any promises. Using potentiometers and a fully charged battery will allow you to tweak your design though.
With a Vin and Vout max of 40V, I would say that the charger can accomodate 3 12V batteries in series so there is threshold variation over the entire range. After you research some of the voltage level charts for lead acid batteries and look at some of the manufacturers data sheets, you may want to adjust your threshold voltage level.
Thanks,