1) It looks like this used be stored in the addon.ini file (see
GMCommands. Now it is stored in the "commands" table in the DB. The "access" column is the minimum account status to be able to use a command.
2) Not sure about disciplines, haven't tested them myself. To be honest, I'm not even sure if they're fully implemented.
3) I don't think there's a setting like you're referring to, but you should be able to adjust a mob's AC, resists, etc to properly tune an encounter the you feel it should be. However, I get the feeling that might not be exactly what you're looking for. But I'm sure that once PEQ or Angelox's database gets to that point, we might see some changes specific to that.
4) It sounds like it could be related to how the server sends the critical messages to the client. It sounds like it would be worth it to sort through the source code to find out how it is sent to the client. For example, it might be sent as an "echo" to the client, instead of an actual "critical".
Hope this helps, or at least points you in some of the right directions.
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