1) The TFTP directory will contain all the necessary files for the MiNet phones, they are included with the system software and must match the version. You can place SIP files there by FTPing to the controller (do not use current FileZilla client because it fails, I use WinSCP), login with the normal web admin credentials... This will place you in the /sysro directory, then move to the /sysro/tftp folder.
2) Depending on your software version, it will be under LAN/WAN Configuration, and you must be logged in as a system user (System or another account with root access)
3) Again, this will depend on your revision, but in either the upper right corner or lower left, there should be button called About, click this and it will open an information window detailing your software version.
4) SHUTDOWN is definitely the correct command, I think you must be logged in as a system user to execute that command.