My JA install dir was to long too, so what I did was just fake it by making a different path for editing and then it worked.
make a following directory structure (just like the game):
(here you make a dir called: Tools and place the modviewer under) (D:\jkt\Gamedata\Tools).
Then make the following dir and place your modelcontent + dirs under it:
(for model Nomak it would be: x:\jkt\Gamedata\base\models\players\nomak)
If you run it now, it will not exeed the max path and for me this worked. ALso you will find out now wheter the other problem also is solved or not