As far as I know, its just an ordinary firewire port. No idea why it on the inside, never seen one used. Maybe thats why the later ones didn't have it.
2001 would make it a Digital Audio or Quicksilver chip. If you've ruled out QS, DA is the one.
Ok, for the last time I will give my suggestion. Cut the ide connector off, besides getting a new cpu, that is the only solution. You are trying to put a DA G4 cpu on a Sawtooth board and that just doesnt work without some modding. Sorry to break it to ya.