Okay, I had to re-edit the installation file - I got the name of the template wrong. I also added the Message Tracking checkbox feature to the Quick PM Reply Box.
If you downloaded this hack before this post was made, please re-download and re-install it.
You can test the Message Tracking checkbox in the Quick PM Reply Box here at vBulletin.org - it works.
Like I said above, the PopUp Message Tracking Window still happens in the Normal PM Reply Page. For Quick PM Reply - there is no PopUp Window - use the checkbox instead.