How to build Li-ion over-discharge protection board
You probably don't need this answer anymore but maybe for future reference.

Available on the Arduino, actually the atmega chip is a bandgap voltage. Basically the chip produces a fairly stable and linear(ish) voltage reference of about 1.1v (it will vary a bit due to temp etc)

This allows you to compare your supply voltage against this reference, without any external components at all just using your Arduino. So a software only solution can be implemented. I've used this on attiny85's.