Because I hardly wanna publish parts of the script, I will just say that alot of lines are included in OnPlayerDisconneect, could that lag the server on disconnect? If it still doesn't help I am willing to post the OnPlayerDisconnect.
If you don't want to publish your script when it's needed, then you won't be able to get any help. It's unfortunately a two way street. If you don't trust us with your code, you shouldn't be asking for help.