IIRC, creating an emergency floppy doesn't work unless you have a High Density Floppy Drive (Great going OS3.9 team).
That's nonsense. You must create an emergency floppy first, anyway. You cannot install OS3.9 from a running OS3.1 system, you have to boot OS3.5 or 3.9 first (well, you can, but you will get random problems like strange-looking icons). That's what the emergency floppy is for. And certainly a DD floppy is totally sufficient.
Then I suggest you install WB3.x either on the partition you're gonna install 3.9 on (and install OS3.9 over it) or make another bootable partition just for running the installation program from which you can later remove. (or keep as a WB3.x partition).
That's nonsense, too. Once you have an emergency disk, you don't need any part of OS3.1 any more. The best way to install OS3.9 is to boot from the emergency disk, use OS3.9's HDToolbox to partition the HDD and install OS3.9 onto a freshly formatted partition. This way you don't keep any old files which might cause problems.
Bye,
Thomas