I’ve definitely felt your frustration here (小皿) and 先日 were particular frustrations. As others have said, it sounds like you might be better off just finding media to immerse with, and learning readings like that (perhaps check out https://satorireader.com).
To answer your question, I largely deal with this sort of stuff via user scripts
- [Userscript] Self-Study Quiz - #20 by pajn - you can filter this by Kanji, Vocab, and/or Radical. So it gives you a way to isolate which reading is which.
- WaniKani Katakana For On'yomi - puts everything ON into katakana, everywhere on the site. Seriously helpful… much more than slightly different background colors
- Wanikani Double-Check - lets you undo/retype a wrong answer. I use this somewhat liberally, especially with rendaku or with any word that’s gotten really demoralizing for me. If I’m having that much trouble remembering the reading, chances are I’m not encountering the word outside of WK anyway. So why waste my energy on it?
- [Userscript] WaniKani Rendaku Information - gives sometimes helpful explanations of why a word does/doesn’t rendaku. It helps if you’ve read that Tofugu (or similar) article on rendaku
Otherwise, sometimes it helps to google a kanji and “when is it read which way” or something like that. There’s often some type of pattern to it. Ex: words - How do we decide if 中 is ちゅう or じゅう? - Japanese Language Stack Exchange . WK just says “oh, it’s rendaku”… but as the thread points out: じゅう is used for expressions covering a length of time (resp. area) from start to finish, in its entirety. I.e. “through”, “all of”, and ちゅう is for pointing a particular time (resp. specific location) out of an interval (resp. general area). I.e. “out of”, “during”. While you might key into some of that on your own anyway, sometimes it’s helpful to have a more formal explanation.
Another thing that can help is to review recent mistakes, or recent lessons and just brute force them a bit, until it sticks. One thing I make sure to do when learning and reviewing is to say the reading & meaning (for extra practice, read the usage examples out-loud, as you’re learning). I also write out a google doc with the kanji + reading, and the vocab + reading underneath it. That lets me see & reinforce them as a group.
As a final thought, you may need to just have a bit more patience with yourself. Sometimes it just takes a frustrating amount of time for stuff to stick. Best of luck!