Memories of 3.1.1 are growing dim now. Seem to remember that the config.sys and autoexec.bat must have the required drivers for a CDROM though I think these can be derived from the installation disks.
I am sure it is fairly straightforward (given the installation floppys.)
You may not be able to boot from a CD but 98SE can of course be installed via a setup floppy. As to whether it is worth doing that will depend on CPU and RAM. I think my first 98 installation had a Pentium 166MMx and as much as 64Mb RAM and it seemed very very OK at the time!