OS 3.9 SetPatch included a ROM-Updates functionality to install new ROM modules on top of the old ones. This functionality is now implemented by a separate program, namely "LoadModule". It is included in the C directory of the Modules disk, or available from Aminet:
http://aminet.net/util/boot/LoadModule.lha
You’ll need this tool to load Intuition V45 (see below).
OS 3.9 SetPatch also included "NSDPatch," a feature to patch-in a Commodore-only command set for addressing large devices, while most third-party devices supported the earlier TD64 specification. This extension is no longer necessary; see above.
If you want continue to use the NSDPatch approach, you find the NSDPatch program in the C: directory of the Install3.1.4 disk. Copy the program to the C directory of your boot disk, and place NSDPatch into your Startup-sequence right after SetPatch.
However, as stated above, this step is (typically) no longer necessary.