How to set keyboard shortcuts from a script

I think you can achieve that effect using a script like this (only deals with switching desktop, but it can be extended changing switch-to-workspace* with move-to-workspace*):

#!/bin/bash
gsettings set org.gnome.desktop.wm.keybindings switch-to-workspace-up "['<Control><Primary><Alt>k']"
gsettings set org.gnome.desktop.wm.keybindings switch-to-workspace-down "['<Control><Primary><Alt>j']"
gsettings set org.gnome.desktop.wm.keybindings switch-to-workspace-left "['<Control><Primary><Alt>h']"
gsettings set org.gnome.desktop.wm.keybindings switch-to-workspace-right "['<Control><Primary><Alt>l']"

NOTE: Maybe the <Primary> part in shortcut is redundant. Try by yourself.

To automate the process you can also make this script run at startup, using the "Startup Applications" program.