Where is the auxiliary input located on a Land Rover Discovery 3 S model the manual has information as to where it is on the SE and HSE models but not the S?

It doesn't have one. Only the SE and HSE (equipped with CD changer).

You can wire up your own AUX input to the stereo head unit. But it will require a little work.

Wire to Pin 7 (left), Pin 8 (right) and Pin 12 (ground) of a connector labeled as C2115 behind the radio head unit.