Unpack the YPF is easy, there are a few tools that can do it. The easiest is GARBro. YuRIS Tools linked above can also do it.Wait, how did you extract, alter and repack the ypf files? All the new games are using the same file type and in the future I want to translate them. Please be as specific as possible on the instructions.
The tool kind of holds your hand. You have to make a 0_ypf directory and put the data.ypf in there. Then hit unpack in the YPF Tool tab. Then you can move to the YSTB Tool tab and follow the order. XOR Decrypt. Then Export. After Export you have to translate the json (I wrote a python script to do that, I think I provided it?). Then Patch.
The Concerto games don't require repacking. I wasn't able to figure that out. You can just put the ypf directory next to the executable and it overrides the ypf file with the ypf directory.