The adapter plate is for a 64-73 Mustang.
https://www.macsautoparts.com/ford_m...op-loader.html
This diagram shows orientation.
http://www.allfordmustangs.com/forum...er-shifter.jpg
From what I see, the top picture you have it correct. Countersunk screws attach the plate to the trans, Shifter attaches to the aft threaded holes on the plate. Effectively moves the shifter aft 2".