There are 6 "candidates" for the John Clark who died in 1890 at age 45 -- only one of whom has a father James. Unfortunately, the mother is Margaret, not Emma.
The 1873 death of Robert Clark, father of James and William -- if he died in Edinburgh, Scotland, he was born after the James born about 1800. If he died in NSW, of the two deaths in that year -one is registered for Liverpool, the other for Kiama.
There seems to be only one possible birth about that time (1800-ish) in Midlothian - James son of James and Elizabeth, born mid-1799.
No Hannah Clark born in NSW in the time frame to be old enough to marry in 1876 has a father named James.
There do not seem to be any children born to James and Emma in New South Wales, Victoria, or Queensland. So, IF there are any children born to this James and Emma, have you considered they were born outside Australia?
I think there are multiple James Clark males, and it is too easy to mix them all together and make them all into a single person who never existed.