I appreciate the response.
The guide deals with how to make your own menu items and icons, how to get more desktop icons in Mate-Tweak, etc. Those are not my issues. My issues have to do with system panel icons in the system tray having non-compliant icons and an icon that cannot be removed (hidden) from the system tray.
Since you are the second person to mention Ayatana to me (had mentioned the messaging icon to a friend earlier) I will point out that on my system at least those items appear to be greyed out.
I am completely unable to manipulate the controls or even see what they are in those sections. I am not sure if this is because they are not yet active or if it is something wrong with my system. I have been operating under the assumption that they are not yet ready as this is an interim release. If this is a bug and those sections should be available to me, please let me know!
Thanks again.