In my opinion, Japanese homophones only become a significant in problem in fairly advanced Japanese, when the proportion of Sino-Japanese words (as opposed to y

In my opinion, Japanese homophones only become a significant in problem in fairly advanced Japanese, when the proportion of Sino-Japanese words (as opposed to yamatokotoba, "native" Japanese) increases. In conversational Japanese it's rarely an issue. Don't sweat it. Just avoid learning 2 homophones at the same day/week so that you don't get confused.