Big big disapointment today

I think I've just discovered that I've been researching down the wrong route

I guess you can imagine how gutted I am as I have done such a lot so far, anyway, I don't know if anyone can help me out here.
Starting with Herbert Darling born approx 1880 in Bradford, on the 1911 census he is in Chesterfield Derbyshire as a lodger and goes on to marry their daughter Agnes Ellis, he dies in 1923 in Chesterfield.
On the 1901 census I have him working on a farm in Yorkshire, and in 1891 he's in 'Nutters Orphanage' in Bradford along with his brother George.
On the 1881 census he is in Bradford with his parents, brother George and two sisters, Grace & Mary Jane who both died 1882 & 1883.
Now here in lies my dilemma, what has happened to his father John? (stone mason) born Scarborough 1851, his mother Harriet dies in 1887, I can find no other records for him, either before or after this census date, no birth, death or marriage.
I had assumed that he went on to marry 'Eliza Glaves', and this is where I am sure I have gone wrong (and this is the line I've been following) after discovering another record for 'Eliza's John' yesterday, which on the 1881 census puts him in East Ayton Yorkshire as a farm servant, so he could hardly be in Bradford with his parents!!
Oh boy, all the work I've done, I'm gutted!
But anyway, getting off on the right line is proving difficult, as I said I can't find any records for the 'right John' I assume his kids (Herbert & George) were put in an orphange after their Mum died, but what happened to John? can anyone help, point me in the right direction or just something, I'm pretty close to giving up altogether I can tell you, I'm so mad, grrrrrrr
Would be eternally grateful for any snippet anyone can offer, thanks.
(Forgot to say that I got Herberts fathers name and occupation from Herberts parish record of his marriage)