Hi Matthew,
I'll propose a different approach. First, use universal IO to mux your pins for PWM. Then just use the PWM sysfs file system to deal with the rest.
So, I have not done this personally yet, but I know it's possible, as I've seen blog posts on it in the past. The universal io part I would probably need help from Charles as I've not that done with universal io either. But I suspect it's very simple.
If you have further question on the subject I can help guide you. As I'd really lie to see people getting away from Adafruits BBIO whihc seems to be abandon ware now days