There must be a way to copy the files needed from the 3.1 install and add the required libs for the 060 to a floppy to make an 060 useable 3.1 install disk.
Just copy all files manually from the Workbench disks, after you have booted without startup-sequence. Then copy the 040 and 060 libraries to libs: and you have your clean install of OS3.1.