Usually, the Wanikani mnemonics, if you’re using them, are designed to partially alleviate this. Remember how they draw attention to “little Kyoto” as きょ vs きょう for “Kyoto”? For the most part, one mnemonic word maps to one reading, like じょう with the long vowel being Jyourm, and じょ with the short vowel being… Jo-anne or whatever the woman’s name was, Jo. Same goes for the third, with どう being doughnuts. If you can identify those consistencies and map the words like that in your head, it helps immensely.
I want to say in the second example that something about long vowel into つ just… strikes me as a thing that I haven’t come across in kanji readings? I’m too new at this to speak authoritatively at all, so someone else can probably chime in there, but しゅうつ as a kanji reading just sounds off to me based on what I’ve come across. Maybe with a little more time you’ll develop that kind of sense, too?
Maybe I’m wrong, but I think that kanji readings for a single kanji never have a long vowel in the middle. Maybe at the end, yes, but not in the middle, and definitely not if the reading is an on’yomi. I’m a little less certain about kun’yomi.
For the rest, I have no real idea how you can remember them, but for me, what I do is that when I learn the word, I make short vowels really short, and I exaggerate the long vowels a bit. That’s not really how you’re supposed to do them, but that makes the long vowels leave a greater impression on me, and helps me remember better. The last thing I’d suggest is writing the readings out by hand, because I find that writing can help with retention.
this happens to me a lot too! it’s very frustrating. one thing that might help is to note the ones that you get wrong often (or use a leech script to do that for you) and take special time outside of the review to go over it again and again. it might help to, during that session, really exaggerate the long sounds but keep the short sounds short. it could help to emphasize the difference between them. saying them out loud and reinforcing the sounds while looking at the words should help a lot as well.
I don’t worry too much about it. I used to make a lot of mistakes with words that end in どお vs どう for example. I’ll just keep making new mistakes but it doesn’t matter because SRS has fixed those issues time after time.
Yeah, I don’t have a ton of ideas for remembering these other than what I suggested. The next level up would be mnemonics, I guess, but WK already has that, and OP can come up with personal ones too if necessary.
In my early WK days when I was struggling with this, I chose to add an additional mnemonic to indicate long vowels: う → undead. So whatever WK’s mnemonic said, I just made whatever characters in it be zombies or vampires or ghosts or whatever seemed most appropriate. It was an easy way to add to the existing story.
Eventually, I rejected WK’s mnemonics and used a person+adjective/activity system for multi-mora mnemonic generation, but even then, the う was undead.