IF you read up on the coaltrol in that section, it explains everything. the MAX is set to 40 (stoker time off/on). Each stove has different amount of stroke, so the 40 could be higher on other stoves. Usually once you set it, you shouldn't have to mess with the settings except for the Temp. BUT, remember. COAL takes time to heat up, it might take an hour to get it going up to temp, then it cranks once hot. I wouldn't vary more than a couple degrees at a time if at all. Its much easier to maintain a constant temp then changing it all the time.
the FR99 is a PERCENT of the max. SO, yes you can get FR99 if the thermostat is not satisfied. If you have the thermostat somewhere away from the heat source, it will keep feeding until satisfied. if the Setpoint is not reached, it will max out the stove and just keep running until satisfied. V3 firmware features