Is there anyway the welcome plugin could be made to welcome a player to the server in a PM instead of globally?
Yes, this is already what it does, but it announces the player globally too. You can change this behaviour and enable only PM by changing the flags parameter :
53
I advise to set 53 (1+4+16+32), this would fit your needs.
Then if the 1 hour limit were to be removed, it wouldn't be spamming console.
I can't understand. Could you be more precise please ?
Also, I think it'd be cool if being able to announce only players of specified groups, such as superadmins or admins and such.
You have the Greetings function for your admins to set themselves their own greeting message, and when they will connect to your server, the bot will automatically announce them by saying the Greeting message they have set.
Just use the command :
!greeting [<greeting>]