Yes, I concede that the yew tree is of great age and may even pre-date Christianity. Its proximity to the stones is another plus and of course the tree and the stones are only now separated by the church wall. Not sure why you feel that the spring is of particular significance - is it supposed to be sacred? The biggest plus for me is the Papal instruction to the missionaries to the pagan Saxons. They were told to re-use the heathen temples as churches, but to destroy the stocks and stones that they worshipped. That alone indicates that stones and wooden objects (stocks) if not living trees were venerated just before the first churches were built, sometimes on former pagan sites.

The other mystery of this place is why there are two churches in adjacent fields.

the megalith still accessible is a veritable 'holed stone', you don't need me to relate the lore of holed stones here? - there was at least one - a famous holed stone - at Avebury a couple of miles away, called the 'Ring Stone', until it was destroyed in the 18th century . . .