I usually copy the entirety of the CHR ROM, search for it in the compilation with a hex editor, and do the same with the PRG ROM, but only searching for the first few bytes of the PRG ROM in case it differs. If for some reason the CHR differs as well, I do the same with it. Copy both the PRG and CHR in the multicart into a new file, and that's the extracted game. Of course, a NES header needs to be added as well.