Thank you so much for trying to sort this out. I am trying to solve this and a few other puzzles for some elderly neighbours and I urged them to obtain the birth certificate before, but they have deferred doing so (probably because they also have several others to purchase and it all adds up). Thus, I thought I would have another attempt to solve this on their behalf - I love a challenge! However, it really does look as though we can't go any further without seeing the birth certificate.
I found a marriage between William Stone and Sarah Cook, BUT it was on 25 August 1846 - after William was born, and it was in Bedminster, Somerset. No sign of a marriage between William and Sarah Beece. However, there was a christening on 24 April 1842 for Hannah and Samuel's child, Ann. It appears the GRO birth index for Ann Stone with mmn Beece must belong to her, since all of Samuel and Hannah's other children also have mmn listed as Beece. In addition, William and Sarah's daughter Ann was baptised in St Philip and St Jacob's on 5th June 1842, so it seems that avm228 is right that her birth was not registered. That brings us back again to the likelihood that William's parents were William Stone and Sarah Cook.....