So I figured out my PWM issue...
The PWM control registers have a feature that requires them to be "unlocked" before writing to them. There is a config bit that turns the feature on and off. Needless to say, I flipped the configuration bit and it started working.
At the moment I am configured for 9 bit resolution, from the scope, that gives me 76kHz, if that isn't fast enough then I will go to 8 bit, and double the frequency, but that's something to look at once I understand how the regulator section responds.
I soldered on all the SMD passive components, all that remains are the semiconductors and the through hole stuff. I am seriously tempted to get the knob working before working on the regulator section, it makes for a very easy way to change a parameter.
I would expect some accelerating progress this weekend.