Hello, per the request of Elmo on discord, I'm posting my solution to either a bug or limitation in the controls settings for the Harrier.
The issue I was having is that I have my Cougar mfd's mounted so they can't be switched (left and right). DCS would automatically bind these for the harrier, but the positions were switched, meaning my left mfd was bound in game as the right mpcd, and my right mfd was bound in game to the left mpcd.
These binds could not be redone within DCS. The entire columns for both mpcds were greyed out and could only be set back to default.
Solution
My work around was quite simple: Go into the Harrier files and switch the names of the lua files for the Cougar MFD's.
F:\SteamLibrary\steamapps\common\DCSWorld\Mods\aircraft\AV8BNA\Input\AV8BNA\joystick
Change "F16 MFD 1.lua" to "F16 MFD 2.lua" and "F16 MFD 2.lua" to "F16 MFD 1.lua"
All that I had to do after that was re-bind the rocker switches in DCS to the correct inputs and all was good!