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Say I have an putnpc command that puts an npc down that clones the player (thru setcharprop <part>,players[0].<part>) would the clone be different for every player, or would it just be a copy of the guy who used the putnpc command?

Depends on whether its an NPC-Server NPC or not, or at least, I think it does, I have almost no experience with NPC Server

yes it depends..
if you want to put a clone of the player it would be kinda messed up w/o npc server, because of putnpc.
Since in the putnpc command you cant pass arguments when it lays (i think) it will show it as them (or maybe as the leader)..
on npc server if you pass the player who lays , his looks then it would look like him

It should look like the player who put it...
if u wannabe sure that a NPC only works for the player who put it down u could use some "paramters" ;) so for example the playersid. Just set the playerid as the image file of the NPC and read it out with #f . normally online the server adds an .gif to the filename but with #e you can substract it. With that id u can check for the right player...