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Ooh, this was enjoyable, even though it took a very long time for the penny to drop! But 13d is stubbornly eluding me, even though I'm sure I have all the correct crossing letters (three of which descending, R,U,and K have been changes as per the code). A hint would be most grateful.

Oops! meant to type appreciated.

13D: 3 letter word for naughty + last letter of dog inside the sort of chair that makes cats nervous. Def is African mammal

Most improbably, the nearest relative to the mammal is another African creature, the elephant.

Thanks buddy. Haven't yet experienced those chairs with cats, but can imagine the scenario

Doh! Just understood the rubric. Can't believe I didn't consider that earlier. Ah well.

I finished this a few days ago, but I came back to this site to see the comments and check if anyone needed help. It turns out I may have needed the help. I found all the substitutions, and thought they were completely arbitrary, but now I discover that there's a hidden Inspector. I have looked again at my notes and the grid, and can see no such name (I suspect it's someone with seven letters in the surname). There is no need to reply to this, but I just thought I would set out my thoughts. in case it helps anyone similarly perplexed.

Pendragon
The substitutions are not arbitrary. Find a word that links the fifth and sixth words in the rubric. Google the latter. Reread the rubric carefully in conjunction with what you find.
Et voila!

Reading the hints with interest. I have assumed all the long answers are entered normally. That leaves me with the 12 short solutions but I can’t fot the life if me see what to do! I assume the connection between the Inspector and coding is the obvious one but am still at a loss. Normally the penny does drop with Genius.

Almost there, in this genius of Genius crosswords. (Qaos’s Magic Square Genius earlier this year was the finest I’ve ever seen). But stumped by 1d, and the first word in 1a…any gentle hints, anyone. Also struggling to find the 15a bird online, although the wordplay suggests it can only be one of two.