It sounds like you'd want two float switches, and some way to connect them to the valve position so that only the switch in the tank that the valve is drawing from will switch the pump.
I am starting to see what you are doing with the riser, you are trying to sense height from the pump side of the valves, it eliminates a lot of electric logic. Another advantage of doing that is if both valves are off, then there is no volume in the riser and the pump won't run.
Simplest "empty" float switch I have seen is a tube with a rising float (hollow tube a little smaller) that triggers a microswitch (can be any kind of switch, including optical). If the tank is empty, the float is on (near) the bottom and the switch closes and lights a signal (you could have it either open power to the pump directly, or trigger a relay). As soon as the float is high enough to turn off the signal (let the pump run, etc) it hits a stop. Water can keep rising as much as it wants after that, you don't care--you don't need it to tell you how much water is there, just "more than enough". Example is from a simple consumer grade humidifier.
Other nice thing about this system is the float is tall enough that the switch itself is well away from the water. No reason that couldn't be a rod that sticks up attached to a float, rather than a tall float. Total travel is about 1/2", if that.