In that case you have to apply the mod through the patch folder where the modded files goes into folder mimicking app0:
Example: Persona 4 Golden has a folder named "data" which contains the data.cpk. Thus the placement of modded data.cpk goes ux0
atch/[TITLEID]/app/data/[data.cpk]
Then you have to modify the param.sfo which you dumped from gro0: not app0: to raise the version level and transfer it back. Some1cp has a good guide.
Use moleculeshell sce_sys as a base and transfer param.sfo from your game into it.
Good luck modding!