I know this is probably related and not related at the same time, but I also had trouble with the kanji in Season 2 for that particular reason. I ended up breaking it down into a 3 prong process– identifying what the main kanji looks like, the reading (sound), and then the meaning (context). If you ever get a deck of kanji flash cards, the information will be broken down like that with the usage on the back of the cards–mostly in compound kanji form. So it means every time you see that compound kanji (using the main kanji), you will have that particular reading (pronunciation). After a while, I’m assuming if you see the compound kanji and read it aloud enough times, hopefully my/your brain will register that as the correct reading…Like your brain will just know what sounds right and what sounds wrong.

Comparing this to learning how to pronounce words in English that are not spelled the way they sound, you would have to memorize how to pronounce it. A lot of weird English pronunciation rules that I no longer identify but I say the words correctly all the time without having to know “why” am I pronouncing it that way. My take on that 1) I either memorized it when I first came across it, or 2)I have heard it pronounced it correctly all the time in common speech. This process makes sense to me because I had a native speaker read a block of text with kanji and hiragana out loud and they did not break their reading rhythm at every kanji/kanji compoud. It was very natural for her to say the reading for the kanji when she came to it and I asked her how she knew and she said “It sounds right, that’s just the way it’s said” and then she added “in context, when it’s used like this” so she must have had an idea of what she was reading, and then she comes across the kanji, and her brain automatically reads it the correct way based on what she’s reading in the sentence. She didn’t get into a whole on’yomi kun’yomi explanation even though that is also very important information to know… but day to day communication, I’m sure no one is thinking is this kun’yumi or on’yomi when they are reading/talking.