You've obviously made some progress since your original post as you now have a place of birth, Ely, rather than just Cambs, and parents' names.

Sensible suggestions:
- Do as I suggested in response to your original post, and ask for a look up on Boyds Marriage Index for a marriage between Smith and Ellington. Now you know christian names as well
- order the microfilms of the registers of the various Ely parishes from your nearest LDS Family History Centre (list at www.familysearch.org ) and go through them looking for a baptism of John Ellington Smith.
- there are two plain John Smiths whose births are registered in Ely registration district in the time frame you specify (see www.freebmd.org.uk/cgi/search.pl ). You could order these certificates from the GRO to see if either is your John - you can reduce the cost by giving as a reference point that the mother's maiden name should be Ellington.

The extra detail that you have now found doesn't help a lot with the censuses. There's no John Smith born 1839-41 in either 1841 or 1851 with parents John and Ann in Cambs that matches.