Welcome :-)
I don't mean to sound patronising or anything, but sometimes it's the obvious stuff that we all miss :-)
There's 2 parts to the installation. There's a "PRE-Installation" then a reboot (back into 3.1), run the installer again and you'll be able to run the proper OS3.9 install after that. Another reboot and you're in 3.9.
I think you only need to create an Emergency Boot Disk if you are installing on an empty drive. You use the floppy to boot from then format/install from there. But if you're installing over 3.1 then you just need to boot from the drive you want to install it to.
