Sorry for the late and long reply, I saw your post earlier and had been meaning to reply but kept being too busy, I just remembered today.
For learning Hiragana (and Katakana) I also grouped similar kana together and combined that with making stories and pictures (like what WK does for kanji).
I used to have a lot of trouble from wa わ, ne ね, re れ
wa is a WAsp, notice the wings
re is a person wREtching over
ne is a kitty cat (NEko in Japanese), notice the curled happy tail
You can find these pictures and more in this article or this chart, there is a longer list of charts here. If you google for “Hiragana mnemonics” and “Hiragana pictures” you’ll hopefully find a bunch.
I combined a few of these charts, trying to find images that stuck well for me, with coming up with a few of my own.
As silly as it sounds I found it helpful to find words that uses these confusing pairs together, For example I kept struggling with differentiating me め and nu ぬ and for some reason the English word menu めぬ helped ?!?
For katakana a lot of the characters are very close, so I made little diagram of their relationships which helped
nu ヌ
^
|
fu フ --> wa ワ --> u ウ
|
v
ku ク --> ke ケ
If you aren’t already you might want to consider flash cards. For kana I used physical paper flash cards to learn them, after the initial phase I switched to Anki (flash card software) and revise a few each day.
I still mix up some characters, but I can usually figure them out from context similar to what I do in English, it will slowly get easier over time.