The existing menu is created in overlay.pyj in the class MainOverlay. Be aware that calibre 5 is just around the corner and it dds annotations functions to that menu (relevant code is in the annodb branch). Instructions for setting up a calibre development environment are here:
https://manual.calibre-ebook.com/develop.html
If you wish add icons for the viewer interface, you add them under imgsrc/srv
In your mockups you have overlooked the back/forward buttons, and what is particularly dear to my heart personally, the clock, as I tend to get absorbed in reading and lose track of the time.