Another approach is to use some sort of mode condition.
loop() {
if we are in limit setting mode
do the limit setting loop
else
do the normal operation loop
}
limit_setting_loop() {
if the "end of mode" button is pressed (released, whatever)
set mode to normal operation
else
if the 'set upper limit' switch is pressed
record the upper limit
etc etc
}
normal_operation_loop() {
if the "set limits mode" button is pressed (released, whatever)
set mode to setting limits
else
do the normal stuff
}