Don't use InstallerNG, it is not fully compatible to the original Installer.
The Installer V44 program is contained on the OS3.9 CD and is installed automatically into both C: and Sys:Utilities. You must have done something really strange for it to be backlevel.
Why do you install OS3.1 at first ? Boot from your emergency disk and directly install 3.9 onto the empty partition. You might even copy the mediator and graphics drivers onto the emergency disk so it runs on the graphics card at once.
Bye,
Thomas
