Thanks! I was able to make it work by converting manually. I noticed that the PSNLiberator also resigns the .self files which is why it doesn't work. I copied the original .self files and there it worked. This was tested for Assassins Creed Liberation HD and Far Cry Classic.
About Crysis, yes I had to wait and it worked after installing gamedata while on blackscreen. Very weird that it doesnt have a notification screen that says gamedata is being installed.
Any chance you were able to make Sacred Citadel work? I have no luck with it.
Also - I used psnstuffx to acquire rap files. Is there a better source? When I tried to load the latest database for psnstuffx, all the rap files were gone. Instead, it is telling me to install the .pkg fix which loads all the .edat. I don't think edat files are needed to convert psn into ISO so I thought it was useless to use the updated database.