Wait, you're learning kanji's, but haven't heard of 訓読み / 音読み? When you're doing it wrong, because it is an essential part of the language.

And I would argue that learning kanji's by themselves makes any sense. You don't have to worry about 音読み at all until you'll find a compound word that uses it (e.g. 山林, 山岳, etc).

It doesn't matter if you know all kun-/on readings at all, since there are words like 山葵 (pretty common one, BTW!) that completely break the rule, so you'll have to memorize the word itself.

So my advice is: learn words themselves, not kanji's.