For a negative booster, there are some pretty big differences. The transistor switches the input voltage, and the inductor is instead always tied to ground. The rest of the circuit is also goofy, with the diode between the transistor's emitter and the positive side of the inductor (the side not tied to ground). And the diode and capacitor polarities are reversed. I also think an NPN wont cut it. It'll be necessary to use a compound transistor (sziklai pair) to control the input voltage.
But, like you mention, regulating it will pose the biggest problem.
In the source code I put a note about using a depletion mode mosfet to convert negative Aout to a positive voltage. I don't know if it'll work well.
There might be a simpler way, too. Some addition to the voltage divider and a pull-up resistor to +5V. I'll have to think about this.