Replace/Add files to the CVMs without repacking.
1. Edit PCSX2_vm.ini inside the PCSX2 ini folder and change the line with 'HostFs=disabled' to 'HostFs=enabled'.
2. Extract the SLUS from the ISO and add the .ELF extension to it.
3. Place replacement files in a folder named after the CVM, which goes in the same directory as the .ELF.
4. Load the game's ISO in PCSX2 (with cheats enabled), and then select "Run ELF" from the "File" menu.