Hello Buster,
I did Aeronautical Engineering at University, so I might be able to offer a different angle to Genghis.
If you approach it from what influences the stall, then it helps to know what the stall equation is:
Vstall = Square root of [2L/(CLmax.S.rho)]
where:
L = Lift force (N) which is equal to the weight in straight and level flight,
CLmax = max coefficient of lift for the wing (can be found on the alpha graph),
S = Wing area
rho = density
I can imagine a simple program that you could use to calculate the stall speed. You could input the CLmax for a given aircraft clean and flapped, input the wing sizes clean and flapped and then you'd just need to measure the density and velocity of the aircraft in flight. You could work these out from a pitot or something similar.
Measuring the lift may proove a tad tricky - perhaps it would be easier to measure the load which could work out the lift (having inputted the mass before take-off?).
You'd then just need to tell the program what state the wing was in (clean, 10 deg flap etc etc), perhaps that could be done with a sensor by the flap or the flap lever.
It might take a bit of design iteration though!!