I recently spent two nights reading this fascinating story, going to bad at 6am both mornings so I thought the least I can to is to leave couple of words feedback to each chapters. It took me longer than I thought, not being native English speaker, but... Regarding the enormous amount of work and time and soul that you put into writing...
Thank you!

'I am trying not to hide' Sherlock, do, or do not, there is no try. Epic fail this time.

I think this is my favourite chapter.
'Snap, crackle, pop' :-) An how John needs more space and time to adjust and mend the two line of memories, the two personalities. 'Almost me was actual me.' I can relate.
And how he is just not able to lie to Sherlock. And what a blessing is it really, that Sh can trust him on that base. I don't think Sh can trust people easily otherwise.

Two Holmeses 'Definitely bloody abnormal' :-)
"Work environment lot less pleasant' :-)
I cherish how this John does things slightly differently than old John, like going to the pub with Lestrade earlier, and losing his temper about Donovan here, I think these changes are for the good and could remain in his personality even after he regains his memories.
'I never left' Oh that is what we all need, don't we?

'Sherlock - whispers John, the hard syllable dissolving into a long groan'
AAAAAWWWW
And then: Frozen, lost... :-(
'I tried to be him. For you'
Such an emotional rollercoaster...

'Toast at 5 am' :-)

'Puddle of darkness on the pavement' :-(

'Got you again' :-)

'Maybe he'll come anyway' - oh how he did...

I appreciate how you write the niceties of the touching session(s). And John's first recalling of what he has gone through, especially how he needs to walk around that place of the floor, oooh...

I like the first bigger glimpse of John's POV, and how Sherlock is practically reading his mind while he is typing :-)

I like how you write Lestrade's reaction to Sherlock's return, down to tiny details like the 'breath after the stairs' and the 'missed the smart-ass'...
And I adore how music can be the first connection to John! And how Sherlock even has written a piece in his head about him.

I like the deductions! Some people try to write Sherlock without them, but...

I so like your Sherlock! IC, more vulnerable but it is understandable in the circumstances, but still very Sherlock.
'I brought you grapes, ate them'
The whole part about dust and skin and old version of John and emotions induced stupidity.

I actually like your take on second POV, and think your Mycroft is spot on.
This part as well: 'I hardly recognise this man' - No - Objectivity - 'You hardly recognise'