I kinda liked the way TextFugu taught the hiragana, it made me understand from an early start the difference between short sounds, long sounds, and the small tsu sounds. I also practiced out loud around the house like a maniac for months while learning new words in Anki.
As with all things, practice makes perfect. @fastriver I’m sure you know this by now, but you can play audio when you learn words in WaniKani, both during lessons and during reviews. I recommend doing that for every word, and it’ll make it a lot lot easier to distinguish between these different hiragana versions.
Just in case you didn’t know:
You’ll eventually reach a point where かこ, かこう, かっこ, かっこう will seem so different from one another you’ll wonder how you could ever have confused them.