I think the key tothis will be to find little John on the 1861 census when he is about 6-8 years old.
Sadly I havent got full access, but there seem to be a few possible candidates in the index around that age. would be good to go through those, and see if any are possibles or if any can be eliminated, bearing in miind that his dad 'john' may be dead, or indeed there is always the possibilty that he was just a made up dad, so we cant rule out any just cos their dad is not John!! of course if their dad is clearly someone else Nye, then I guess they can be ruled out. If you follow me.
Anyway - hopefully another rootschatter with full access to 1861 will pick this up. If not, I suggret you try a specific 'look up' request on the Sussex 'look up' board for a look up in 1861 for John Nye born 1853-54.
Hope you find him!