I'm good with you using the calibre UI for shortcut config. Note that the preferences widgets are designed to be embeddable, so you could embed the keyboard shortcuts widget in your config dialog. See for example show_config_widget() which embeds a preferences widget in its own QDialog. It should even be possible to highligh/expand the shortcuts for your particular plugin when doing so. There may be a few gotchas with doing this, but I'll be happy to help smooth them out
