Oh - wow. I am not through reading, but I'm trying to comment without looking ahead and spoiling myself:

Beneath the cuff of Sherlock's shirt, John could see the nearly-faded stripe of bruises in the shape of fingers; faint, long yellow smudges on his throat when his scarf loosens in the wind as they wait for a cab; John fancies that his fingers would fit them as perfectly as a key in a lock.
That is incredibly sexy!

typo: Once in the flat, Sherlock retreats to John's computer without commentary. Knowing this is not a dismissal so much as a holding pattern, John makes them tea; by the time it has finished seeping, Sherlock is sitting back with a faint frown and the blue eyes are fixed on nothing.
should be -> steeping

And now that sexy line - and the animals - and the needing to be noticed - and Mrs Hudson's reactions has me thinking that Watson has had a psychotic break and is the serial killer. I don't know, though, whether you're going to go for that and milk the hell out of it or whether it's going to be a suspicion that everyone will think about, especially John, that will only be disproved later.

But, oh wow, you write that edge of crazy so well! I love that there are so many fandoms well suited to that.