Sorry for the delay. Missed your post!
re John b 1832. Yes, it could be that he was born in Upwell and assumed his birthplace was Ely because he moved there at a very early age.
re John b 1809. It's an almighty coincidence that he married in Terrington and there was also a John baptised in Terrington at the right time. Yes, I think it was the same John, but can't prove it beyond doubt. I don't believe in coincidences.
re the Bedford middle name - I thought I'd covered this in my post of 2 Oct 2013 10:45PM. Sarah Ann Bedford was a widow when she married your Bonnett. Sorry, can't check the census just now as I've not renewed my sub to Ancestry in protest at their imposition of a new search, which I find to be totally useless. I keep forgetting that it's now an "experience" not a seach.