I agree with your conclusion that William Sheppard of Steeple Barton was the son of William Sheppard of Littlecote died 1546. I have spent a lot of time working through wills and other records, and my hypothesis is:
William Sheppard of Littlecote d 1546 had 3 sons - William Sheppard of Steeple Barton, Thomas Sheppard of Hockliffe, and John Sheppard (who had 3 sons, but who I've not been able to trace further). Littlecote passed in due course to the William Sheppard of Littlecote who died in 1597, and then to the latter's son Baldwin. I believe this William was the son of a brother of William d 1546, probably called Thomas. Furthermore Baldwin stated in one deed that his father was William Sheppard, his grandfather was Thomas Sheppard, and his great-grandfather was William Sheppard. This would mean that the father of William d 1546 was another William Sheppard. This ties with the will of William Hoode of Crendon in 1489 which refers to William Sheppard the son of William Sheppard of Littlecote, aged under 22 at that time.
Thomas Sheppard of Hockliffe was the father of Thomas Sheppard of Maulden died 1607, and the latter's son, also Thomas Sheppard of Maulden, bought Littlecote (or rather, the part known as Chalfont manor) from Baldwin Sheppard.
William Sheppard of Steeple Barton left 2 young sons, John Sheppard who was in chambers at Grays Inn but also lived in North Aston, and William Sheppard who founded the branch at Great Rollright. I am currently trying to work out how these families were related to the Kendall, Methwold, and Swann families. Did Alice the widow of William of Steeple Barton remarry?
I would love to exchange more detailed info.