Follow the same process from the introductory tutorial to package the Unreal project's cooked assets.
In this case, your “FinalPackaging” folder structure will look like this:
FinalPackaging BloodstainedRotN Content Core Character P0000 Mesh SK_P1000.uasset SK_P1000.uexp
It should not contain any of the .uasset or .uexp files that contain the materials, physics asset, or skeleton. Remove those. Only leave the files related to the model edits you made.
Drag & Drop the “FinalPackaging” folder on top of “UnreakPak-Without-Compression.bat” to generate the .pak file. Rename it so it loads alphabetically after “packmod”. I named it “~MiriamBodyMod.pak”.
Copy your generated .pak file into the Bloodstained Ritual of the Night\BloodstainedRotN\Content\Paks folder. Run the game to test.
If you face Miriam left or right while aiming a Directional Shard, she should use the arm that's in the front (like the original game). If this is broken, you did not follow the step to generate the mirror table properly.
If you open the menu screen, the 3 changes I made: