@Ben,
Glad to hear you're enjoying your NovaDrone. Sorry to hear the LFO isnt working. Please feel free to contact me if you want help debugging that. As far as LFO depth is concerned.... there's no simple way to change that. If you are up for some real hacking and rewiring I can explain it. There's a description of how the PWM is achieved in the theory manual here:
http://casperelectronics.com/finished-pieces/nova-drone/theory/#2.2
This will give you an idea of how the LFO is used to modulate the pulse width of the audio wave. It should also give you an idea of how that feature can be modified.