Hmm sounds like dejavu. 1) install OS3.1 on boot partition. 2)install cdrom software. 3) run OS3.9 install (Install over empty HD or 3.1, I forget pick the one thats there. 4) check WorkBench for missing or uncolored icons, if none, skip to 4) if so, then repeat 3) Now add all other stuff important, ie Cybergraphics, reinstall favorite CdRom package etc. 5) Now make boot disk.
should be ready now for everything else. Give her the once over for the last time your done, enjoy
Chris