Touchpad
This depends on what you use to configure the touchpad. For a Synaptics touchpad, you could use the synclient command line tool to save and restore preferences. Other preferences probably get saved somewhere in the dconf database, and you can use gsettings to save and restore those.
Example of Editing Mouse Config using gsettings: 
gsettings set org.gnome.desktop.peripherals.touchpad natural-scroll false
WiFi
Network Manager settings go in /etc/NetworkManager (and connection setting specifically in /etc/NetworkManager/system-connections). This directory requires sudo access to modify from the command line. The nmcli command line tool can be used to automate configuring network connections to some extent. 
GNOME Shell extensions
From the GNOME wiki:
Extension Preferences
Since version 3.3.5, Extensions may be configured in a consistent
  manner using the gnome-shell-extension-prefs tool. To hook into it,
  provide a simple javascript file called prefs.js.
It doesn't look like this is meant to be used outside of extensions, and I don't have a GNOME Shell on hand to test with, but gnome-shell-extension-prefs seems to be your best bet to get and set extension preferences.