you may also want to check that you added customs correctly, both in idnum and num tables. So If the person that died has custom items on, then this would be another place to check
I usually just have my data folder structure so data/wav (and the files in the wav file to be patched). Use thor patcher and point to my grf to be patched. Use the Directory option and select your data folder and generate the thor patch
you should be able to patch it with thor yes. I would actually just use patch single file option and then specify /System, then I don't see why that won't work