I don't see an Edward as son of John either. In 1881, John was a widower at Bryn Nantlech and seems to have the children, except John, with him. Could Edward be a brother? Also, there's no mention of David and the daughters as beneficiaries. Probate entries usually just mention the executors. I would have expected John and David to have been mentioned as executors/elder sons. Have you found them in later censuses?
Gadget