The sonar plugin only allows changing 8 function buttons.  Is there a way to do all 16?

There are only 8 listed, F1 - F8, the others are assigned already.  There maybe some code you can edit somewhere  see the forums member AZslow as he is working on his own way to control the MCU in SONAR.

My MCU preset is mimic the original, that was more just a proof I can configure AZ Controller with such complexity... It is untested for real use since I do not have the device and there was no users to cooperate with, and so I can not recommend it in the state it is now.
 
On the other side I can mod the original plug-in (I have published one mod for PC EQ/Comp control). So I can add/remove something there.
 
But on pictures of MCU I see only 8 F buttons... that is why I have not answered before