Id like to comment on this Server tool. I like the idea and i think you have a great start and outline. Love the chat logs, and the kick/ban for spawned only items/blocks. But i do have some issues id like to see if you can add...
Clans - At first i was excited, then i was not. The clan as far as i tested does nothing for game play. Nor can i see anyone in the clan, nor does it matter if im in one. Maybe you can make the clans useful by adding maybe a /clan whois to see who is in the clan ur in. Also maybe a /c <message> for only clan members to see your messages. Based on what i saw already within the Server Tool, i think this is possible. We need the clan system to be a useful addon. As of now i dont see the point of using it.
Home - The /home command works other then it teleports you underground. I think maybe adding a variable that add +1 - +3 to the height. your choice, would fix this issue.
create custom trigger messages - Something is wrong here because, i put 3 messages and with a trigger and only the first worked the rest never did.
Auto messages - I would also like to see a settable time for each individual commands that we make.
Admin speak to all - i think it would be nice to have the admins name next to the message he send through the server. This help other admins know the source of the message.
commands - i would like to say with the /commands and /help - i think you should use a @ instead of the slash because other managers use the slashes and having /commands and /help that cant be modified is kinda a turn off, because my manager uses them.
Overall you have a good start, keep going with this.