I do a pretty good job of understanding and learning the translations and definitions of vocab words, but I really struggle to remember when I’m supposed to do じん or にん for vocab that has 人 in it. Or when I’m supposed to use にち or じつ when 日 appears in a vocab word. For a kanji that only has like 3 or 4 vocab words it’s not too bad, I can usually brute for memorize it in some way but for the really common Kanjis, is there a rhyme or reason to them? Like how I’ve realized 物 more often tends to be ぶつ when it’s being used in a vocab word where it’s an organic substance and もの when it’s not. Is there any other tricks or rules I might not have noticed for these common Kanji?
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There’s probably clever ways to memorise them but honestly, it’s just a case of using them lots and lots.
Same way you know to pronounce though, rough, plough differently; through years of exposure.
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For 人 there are rules of thumb for sure. The にん-reading, is used when the kanji before 人 describes the actions of the person, for example someone’s occupation etc.
When the じん-reading is used, it instead reveals the attributes of the person, for example their ethnicity etc.
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The hard and fast rules for 人 are
じん - for nationalities
にん - for counting people (other than 1 or 2 people)
The にん for actions is accurate for certain words that were formed that way, specifically when it’s a suffix on another existing word, but there are じん and にん words that don’t fall into that as well. Like, 詩人 (poet) would presumably be しにん if it were about deciding by action, but it’s しじん. Being human is surely an attribute, but we aren’t じんげん. 
For many words it’s just a matter of when the word entered Japanese.
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These are painful (I still have a few that I am getting wrong in new words I’m learning a decade in because of different readings of 人), but essentially my approach is “learn the vocabulary”. I make these errors when I don’t really know the word yet and have fallen back on “guess the reading from the kanji”. Words I really know are the ones I know how to say as a single word and where I’m not thinking about kanji readings at all.
That said, there are some rules of thumb that can make for better guesses (largely around on-yomi vs kun-yomi combinations).
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Make a stupid mnemonic just for this. There aren’t many that are like this and are common. Basically the two you’ve mentioned are the biggest issues. 日 fsr stucks for me without an issue, but I used to have an issue with 人 for quite a bit. I remember someone saying, that they memorize it by thinking of them as people who drink beer and those who don’t. Not sure which way it went, but it would work.
I personally try to sort them as who would be stereotipically strong or weak. Like for murder, 殺人, you would obviously need to be a strong person to kill someone, therefore じん, but if you think of a cook, 料理人, cooks tend to be big and round, therefore they’d be weak, so にん.
Whatever you do, if you keep it up and you reason about it enough, it will work out.
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No hard rule. You get used to it when you see certain combinations.
本日 (ほんじつ) vs 日本 (にほん・にっぽん)
As 人 and 日 are used everywhere, you have plenty of opportunity to practice. So yeah, aside from the tips and tricks, give it some time to soak up.
i agree with this. once you start seeing them a lot you can just recall what they might be. Based on the vocab too you might be able to guess what the reading might be.
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I always come up with extra mnemonics just for these situations. For example, with 人, I try to still use one of Nintendo/Jeans and make up a new mnemonic.
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