I really should update that thread, now that I’ve had a few months experimenting with the system I evolved.
Basically, it’s as you said, with 2 mora patterns, there are really too many for easily making up enough unique ones and remembering which is which, since none of them come up enough to reinforce.
So I changed to a single mora system similar to what @Rowena came up with. There’s a little less than a hundred of those which is far more tractable. I gave each mora two symbols. First is a character, second an object. Each is chosen for association with the sound, either through their name (Gandhi -> が) or because of associations (The Joker -> は; Santa -> ほ, etc). Second is an object, activity or trait. Many times the character and trait relate to one another (Bigbird and yellow -> き) but other times they’re just each chosen for their association to the sound.
When dealing with a reading, I start with the character for the first mora, then actions for the second and following. If there’s four or more, I’ll split into two characters, but that’s rare for single kanji.
I have some special case mnemonics for very common 2 mora cases, mostly borrowed from WK, like ken the squid, the cyborg, the djinni and the ninja. This is partly because they were so solid since I didn’t use my system until later, and also because they’re so common.
I have two specific mnemonics only for use in vocabulary. One is for gemination and the other for rendaku. I find this is easier than trying to override the default kanji readings. Changing Bumblebee crying like in a Peanuts comic (かわ) to Gandhi crying (がわ) caused too much mental friction (much like the 人 issues everyone has), but it’s much easier just to add Puck (my tricksy little rendaku faerie) to the image and be done.
It isn’t a perfect system. It does take some effort to set up, and sometimes the stories are hard to create. What I have been doing is when doing a lesson, I look at the reading and the WK mnemonic and the character/action combos my system generates, but don’t put effort into an elaborate story until I miss during reviews. Sometimes all it takes is knowing Baby Yoda is involved (よこ. I got very lucky on that one, since they were both picked way before Mandalorian was out) and I’m good to go, without even a story for why he’s involved.
Anyway, probably more than you need to know. It comes in very handy, like around level 10 where WK uses ‘car’ as a mnemonic for like 3 or 4 different kanji, each with different readings. But it’s a lot of work at the outset. Good to have now, though.