PeteG,
Perhaps the holes are smaller because, learning from their previous mistakes, they checked the holes regularly, and realised their mistakes sooner.
Just a thought,
TE.
There are photos in Hawkins' book Mindsteps to the Cosmos which show the holes as being 3 inches across.
He speculated whether they could have held wooden markers to measure astronomical alignments.
Could the fallen lintel with the double holes have been reused from a previous monument like the bluestones were?
PeteG