In mine max NPCs are set to 5000 (most probably because I changed it to save some memory

)
Btw, even though when you sum up all monster amounts in each map.txt they keep respawning at first, but as soon as all the monster spaces are filled in the server its pretty dificult you get some zone respawning. That is due to the fact that each server has pretty few players that kill monsters in other zones, and that is why is better to have several game servers with zones divided IMO.
And about item duplication due to changing server or waiting for server crash, the best solve about it is to change the code (once again) and save both player profiles after each trade.
Good luck with your server