1)The question John asked (him) was who did Mary see yesterday
2) What John asked was who did Mary see yesterday.
Are These constructions o.k as 'focused versions' of the sentence 'John asked him who did Mary see yesterday'
These are awkward because subject-auxiliary inversion does not occur in embedded questions in English.
Question: "Who did you see yesterday?"
Embedded question: "I asked who you saw yesterday."
So you can embed those, but the word "did" should be removed (and lexical verb changed to past tense).
I have noticed some non-native speakers doing this (including one linguistics professor of mine!), and it is of course intelligible, but it's not a feature of standard American English at least.
You could put the embedded questions in quotations and have those be direct quotations rather than indirect (paraphrased) quotations and that wouldn't be so bad, but it still sounds awkward, especially in writing.
3) What John said was whom he saw yesterday
That one
is formed correctly, as I would say it.
(Note: whom/who is an optional distinction here that only a minority of speakers would make and usually only in formal discourse.)
Clarification: this sentence means "John told me the name of the person who he saw", not "John asked me a question..." (etc.). So that's more like a headless relative clause than an embedded question, I guess.
