A few more：
泉 いずみ 出水 Pretty big sound change but the reading 出水=いずみ can still be found in names
港 みなと 水の門
鋼 はがね 刃金 This one is one of my big leech in Wanikani… why didn’t I noticed before 
And it’s even a valid reading !
About metal, nowadays for iron and silver the onyomi is used but apparently they have kunyomi too :
鉄 くろがね 黒金
銀 しろがね 白金
And finally a few recursive one
鸛 こうのとり 鸛の鳥
鋸 のこぎり 鋸切り
Nice one! Hopefully this helps you crush that leech!
I just remember 鋼の錬金術師 and it’s easy. 
That comes from しらひと. My guess (amateurish as that may be) is that the ひ somehow triggers the same kind of phonetic changes that い would. I’m thinking of how ありがたい goes to ありがとう, おめでたい to おめでとう etc. and it seems like a similar transformation. It’d help to study some linguistic papers on this, if only I knew how to find one.
The dictionary I’m looking at says it’s the meaning of 白人 > しろひと > しろうと.
In that case beats me. I tried ¯\(ツ)/¯
軛 (くびき) = 頸木 (valid spelling).
This word makes a lot of sense to me, so I like it
頸 is just another kanji meaning 首.
Honestly I was struggling so much with the reading of 傾く (かたむく) - to lean, until this thread helped me realise it’s just 片向く(literally to tend to one side). This whole thread is super useful
Edit: and also fun
捗る = 果取る (valid spelling)
I just find these in heaps while reading, it might be better to just edit this post for stuff I find today instead of making a new one every time.
Also: 銅 is 赤金 あかがね
I came across 陥る, which has 落ち入る おちいる as a valid spelling too.
Oh, I always assumed that one came from someone lengthening the い sound of a normal 落ちる as they fall into a hole.
おちいいいいいいいいいる… る… る
Maybe split into two separate lists, distinguished by whether the origin is a valid spelling?
Also, あいうえお順 would probably make finding stuff easier.
Oh my god that’s going to be so much easier to remember now
Edit: 傾く 傾げる 頷く 蹲る and other words that my brain groups together as “those words” are the bane of my life
I have nothing to add, except that 遡る has been my favorite of these for awhile.
導く as 道引く?
I don’t see it listed in the dictionary.
I noticed that and use that as my way to remember, actually, but hadn’t really thought about it. Nice catch.
You all are expanding my mind. A whole new world.
Edit: This suggests it is
Interestingly, it turned out that 断る (ことわる) and 理(ことわり) come from the same origin 事割
Can someone please double-check these two items?
| 〆 | しめ | 占め | Not valid spelling |
| 詔 | みことのり | 御言宣り | Not valid spelling |
The origins come from Wikipedia/Wiktionary but they don’t cite any source.