Apply the xdelta patch to an unmodified Nayuta no Kiseki ISO.
Some useful xdelta patching tools:
Select the xdelta file you downloaded when prompted for a "Patch". Select your Nayuta no Kiseki ISO when asked for a "Source" or "ROM".
Be sure to supply a name for the output file that ends in ".iso" or ".ISO" so that the patched file is recognized by PSP CFWs and emulators.