I’m not sure how to save a custom menu that I have hotkeyed, so that it returns (both the hotkey and menu) when I restart zbrush. How do I do this?
There is no way of saving out custom menus to a file? Or having those custom menus sub options persist when you reopen zbrush? I added a bunch of deformation and masking tools for a quick recall, however after the restart of zbrush, the menu has nothing in it.
You need to save the UI configuration. The simplest way is to press Shift+Ctrl+i. This stores the configuration as your default setup so that it loads every time you start ZBrush. Alternatively you can save a configuration as a named file through the Preferences>Config menu Save Ui button. You can then load it again later.
Hotkeys need to be saved separately through the Preferences>Hotkeys menu. The Store button will save the new hotkeys so that they load each time. With the Save button you can save a hotkey set.
NOTE: some items will not stick in a custom menu. Only those items that are present when ZBrush starts and don’t rely on a 3D tool being selected can be used in a custom menu. That means masking and deformation menu items can’t be used. 
Bah! I hope they fix that next update. I think it would a huge workflow enhancement to only access the tools you need, with a key combination.