I finally got it to display within Plex, here is how I did it:
First, place all your specials into a single folder within your folder that houses all your regular episodes. Use the following naming convention:
Doctor Who 2005 S00 EXX
EXX - Refers to the specific special
For example: Doctor Who 2005 S00E02 refers to “The Christmas Invasion.” S00E04 refers to “The Runaway Bride.” You must use the TVDB episode numbers on the left hand side of that website to properly match them up.
Once this is complete, simply refresh the top-site of Doctor Who, and you will now see in Plex all those specials.