SMPS control components and technologies
Not really an answer but a "what would I do"

I used to work for a department where many bright people worked for many years to design a microcontroller based DCDC converter. They could not get it to work properly under all circumstances ! For sure the demands on that design were more complex than yours.

The reason why I bring this up is that I doubt if it is a good idea to try to implement this with an FPGA or microC. instead of using a dedicated SMPS controller. For sure that would be far easier and above all SAFER ! 

Of course the decision is yours but I know what I would do (use a dedicated SMPS controller).