I think there's a broad consensus here that what you're doing is pointless. I know there's a handful of people who have their reasons for learning onyomi separately, but by and large there's not much point in learning onyomi separately from the vocabulary that they appear in - i.e. just learn words, not sounds. As you're discovering, there is no 'right' onyomi - there is just the onyomi that is used for any particular word, and that is for all intents and purposes arbitrary.
