David - yes stauros originally referred to a palisade stake, which would
seem, if anything, to make it the likely candidate for the upright, if
the words stauros and ksulon had different referents. Ksulon, in turn,
once could refer to a wooden stock-arrangement for criminals, over the
shoulders, which could make it more like the crosspiece of a cross
(especially if the hands were bound to it).
But in Koine ksulon had obviously undergone a significant semantic shift,
since it seemed to be an almost ordinary word for tree in the
Septuagint. Stauros may have done the same. Classical etymologies might
be less than useful here.
On the subject of John: yes he was the only one to refer to the nailing
(although not even he at the crucifixion scene). And yet he is also the
one to make the point about "him whom they have pierced" (the prophecy,
which is alluded to again in the Apocalypse). But he does so in
reference to the piercing by the spear in Jesus's side. Why wouldn't the
nails have counted as piercing? Strange.