So, I have played two games in Japanese so far and read a small number of texts/books before I found WaniKani. I spent a LOT of time drawing kanji into Google Translate before I could get the kanji I wanted, before writing out an entire sentence to get the meaning of what I was reading if I didn’t know (often I would know the sentence but I didn’t know the kanji readings). It was this process that lead me to WaniKani in the first place, after spending a lot of time on Jisho.org.
So, for me, it is not imperative that I remember the exact meanings of every vocabulary word or even kanji, as long as I can find it when I do contextual studying without aid through books and games and TV and so on (note; I do not count the dictionary as aid, I find that the process of looking up a word helps to make it stick and after a while you will not need the dictionary). If I am in any position to advise on anything, I would say to adopt the same mindset.
I say this for two reasons:
Effectiveness - going through all your burns again and again with custom scripts is never going to be as effective a learning method as encountering these words “in the wild”, you have sort of already proved this and I have long suspected it will be the same for me. The good news is as long as you know just one reading of a kanji you can look up the word and the chance of it sticking the more you encounter in the wild is far greater.
Your time - At some point in your journey you will have to learn from these “wild” native resources by way of consuming that material without any aid. You can do it now, as a non-fluent, and learn from the experience despite it not being as ‘fun’ as when you have some form of aid. Or wait until you have rinsed every study book and learning resource out there and then dive in. One of those roads is shorter than the other, and arguably not as grueling, but certainly takes just as much effort.
This is just my opinion, and everyone learns differently, but I’m certain that this method would work for everyone. So many famous Youtubers who are great at Japanese (i.e. not Chris Broad) learnt through immersing themselves in native material and spending hours going through them to drill in meanings and nuances.
I hope that helps in some way, happy to discuss with anyone that has thoughts on that because I would also like to learn from other people’s experiences!