I think the Hermes cIOS installer didn't use your WAD files, it use the files in sd:0000001\ and possible some WAD's like IOS202.wad.
That should be in the ios202-222-223_offline-installer.zip. Extract all files to the root of your sd card and start the installer.
Select the cIOS u like to install, than select the IOS and you are ready.
Example:
Install cIOS 222 with IOS36
Install cIOS 223 with IOS37 merged with IOS36
That work also for uloader and that's all.