SetPatch is one thing, but what about the "AmigaOS ROM Update" file it uses, is it present in the Devs drawer of the Emergency Disk, and does it have the correct name? Also, I don't think using a different version of SetPatch is such a good idea, since it might lead to a conflict when SetPatch is run for the third time (from the CD) upon booting.
I have a feeling that using the default OS3.1 CD file system might be the root of your problems, since this will only use the 8.3 file & dir naming method, which leads to certain file names being truncated (and the extensions as well). This file system is only to be considered as a "better than nothing" type of solution. So after making sure that it's possible to access your AmigaOS 3.9 CD, you should have just copied the CacheCDFS file to the Devs drawer on your Workbench partition, and then tried to configure a proper mount file which uses it.