I got the PWM code to start working, at least when viewed in a logic analyzer. When I tried to put the top board on the bottom board and see if it works nothing comes out. The output pin is toggled, the PWMs are running but no output comes from the device.

This may be also due to me wiring it once in reverse (the top board was upside down) so I may have destroyed it somehow. I'll try to debug this tomorrow with another unit that I have and see if and which part is damaged.