For the にん vs じん readings, I’ve been extending the mnemonics to try to sort them out in my head.
For example, everything with the にん reading, I’ll add a little story that incorporates Nintendo (I think this was used in the WK mnemonics early on, and I’ve just kept using it on later words). So for 人気 , I make up a story about how Nintendo is super popular. A couple levels ago, I had 商人 (merchant), and the only thing this guy has in his shop are piles and piles of old Nintendos.
On the other hand, if the reading should be じん, I come up with a story about a person named Jean, who thinks that Nin would be an absolutely terrible name for a person (like, really, are you trying to name them after your Nintendo? Jean is very angry about how rude this is … Also, my apologies to anyone who happens to be named anything similar to Nin…).
So, the 主人 is obviously going to get upset if you don’t know his/her name, and accidentally call them by the name of your gaming system. Or for something like 人格 (character or personality), I think of it like this: people (who could be named Jean) can have personalities; Nintendos can’t (because they’re machines, and that would just be stupid…)
Unfortunately, a lot of it is just memorization, but sorting all of the new 人 words I come across into these two categories (person or Nintendo?) and making up a story about that has definitely helped me keep them straight in head.