first, NEVER put ANYTHING in /freespace, /freespace/data, or /freespace/mediavps. it WILL screw up the game.
create a new mod directory in your freespace folder, for the purposes of this, name it 'nawyriamod', you can change it later. make all the directories (/nawyriamod/data/maps, /nawyria/data/models, etc)
put all the stuff in there (make sure any table files are either a modifed vanilla tbl, which has all the stock ships, or a tbm, which just adds stuff on.)
now, create a shortcut to fred on you desktop. right click it, go to properties, at the end of the directories, press space, and type in -mod Nawyriamod, mediavps
that SHOULD get it working.
EDIT: UGH, double clicked the post thing, never saw the new reply bit...