For v7 of the Mac mini OS 9, not v5, I can think of...
Most extensions are CPU 5.9, one is Z-5.6, and the ROM is 5.4
Modified files:
System Folder:Mac OS ROM
Changes: Edits/Patches to various parts
Reason for Changes: Allow the Mac mini G4 to boot Mac OS 9
Version: 9.6.1, CPU Software 5.4.
System Folder:Extensions:ATI*
Changes: Patched/Edited ATI extensions.
Reason for Changes: Enables Hardware/3d/2d acceleration and probably other graphics related things
Removed files:
System Folder:Control Panels:Energy Saver
Reason for removal: Replaced by Sleeper.
System Folder:Control Strip Modules:Energy Settings
Reason for removal: Replaced by Sleeper Strip.
Added files:
System Folder:Control Panels:Sleeper
Reason for adding: Only sends display and hard disk to sleep, when told to sleep, and not the CPU. (get's rid of not waking up issue)
System Folder:Control Strip Modules:Sleeper Strip
Reason for adding: Replaces the Energy Settings strip, more or less same functions, but works with the Sleeper control panel
System Folder:Scripting Additions:Sleeper osax
Reason for adding: Think this works with Apple Script to work with the Sleeper Control Panel functions