See below link for new tool ready to work with ISOS. Rename to RAR and extract.
The tool will automatically generate 2 ISOS if needed and recognizes all CPS3 CDs.
Regarding SFIII-2nd the tool is prepared to support a decryption table so it can be reconverted for each cartridge.
No time yet to release a proper TXT file. As stated in the source code, this is released as GNU General Public License. If you release a new binary, you also have to release the source code so others can enjoy your change.
A new version with nice menu for Windows in Visual C++ will be available soon.