If you already have the ability to copy files off the OS 3.9 CD and your main goal is to get OS 3.9 onto your HDD, why don't you just
copy amigaos3.9:emergency-boot/#? hdd:
copy amigaos3.9:os-version3.9/workbench3.5/s/startup-sequence hdd:s
?
Or why don't you use your A1200 to create an OS 3.9 emergency disk and then use it to install OS 3.9 on your A4000 ?
Just copy the 68060 libs to the emergency disk and adjust devs/dosdrivers/emergency_cd to match your A4000's cd drive.
Why do you bother with WB 3.1 disks when OS 3.9 is your goal ?
Bye,
Thomas