First of all, I have to say I very much agree with @darkness_rising that your target audience is not really clear. Your writing seems to jump all over the place in that aspect and makes it harder to engage with. Figuring out who exactly you’re writing for and making adjustments to suit that audience would help people make more sense of your guide.
Another thing that makes your article a little jarring to read is that it seems to project an attitude of “This is how you learn Japanese and any other way of learning isn’t going to get you anywhere so only follow this guide and nothing else if you want to see progress.”
Everyone learns differently, and combinations of resources that worked well for you may not work for someone else. It’s helpful to provide tips and tricks for people who don’t know where to start but you should make it clearer that while these resources helped you, they themselves may find other things more useful and that’s okay.
Regarding the Dr Moku app for kana, there are definitely free alternatives out there that can work well too. I myself used an app called Just Kana on android and it was great for quick rote memorising (I don’t see an issue with rote learning for kana because once you know them you’ll have so much exposure through textbooks and reading materials that it really won’t matter how you learnt them). Also, considering that learning Japanese to any degree of fluency is going to take years, spending an extra week or so on learning kana is a just a small drop in the ocean really.
In terms of Japanese pronunciation, I would not say it’s particularly difficult or confusing in comparison to English. Once you can read kana, you should technically be able to read aloud any text that has furigana over the kanji. Of course, that doesn’t mean you will understand what you’re reading, and your pitch accent will likely be off, but disregarding that, Japanese pronunciation is usually pretty consistent and the way something is written is how you would say it when speaking.
When it comes to reading, I agree with what you say about consuming native materials to learn, but you can definitely start doing that before level 40. Even at level 10 you can make an attempt at Graded Readers if you have some very basic grammar under your belt. It’s not native Japanese but you have to start somewhere, and when you do jump into reading your first native material it’s likely going to be something aimed at children that you probably won’t find particularly engaging or interesting. Sure, we’d all love to be able to read a VN, or a Japanese novel, or our favourite manga series. But you can’t start out with that material at a beginner’s level because you won’t even make it past the first sentence.
In regards to your comment about not needing to use WK past level 40; I haven’t made it that far yet so I can’t make any claims on how useful the content is after that point, but considering you’re writing this on a forum of loyal users who swear by WK’s teaching methods, you might find yourself on the receiving end of some pretty strong criticism for saying so (particularly since you have not made it that far yourself yet either).
It might be better to make the suggestion that it’s okay to slow down after that point and direct more of your focus towards consuming native content and grammar study, but when you’ve already made it that far there’s not really much point in stopping completely. Even after finishing WK you’re not going to be able to understand a thing if you didn’t study any grammar. That being said, 2, 100 kanji and 6, 000 vocab is no small gain from a single consolidated resource and as long as you are making time for other things as well you will learn a hell of a lot.
That’s all for now, I guess. It’s just my (very long) opinion FYI, don’t feel like you need to agree with it or anything 
