Where do the metal O-Rings go in the gasket sets. I have looked all over the parts fiche and have yet to find where they go.

I am not sure if they are actual o-rings for sealing, but they are shaped like o-rings but are made of metal.

Post a picture and someone will be able to identify it straight away.  Sounds like the sealing washer for the oilplug that collapses as it screws in.  But difficult to tell without a pic! 

Header pipe gaskets?

What size are they?

The only metal o-ring/seals are the (2) exhaust gaskets at the head and the (4) rubber o-rings that have a metal washer in them that fit on top of the cylinder around the outer bolts.

Here is a pic of these o-ring type things

It looks like the oil drain plug crush gasket.


NOTES:
ID = OD - 2R = 19.8 - 2*2.9 = 14mm
(As expected, based on memory alone, this value would seem to match the threaded diameter of the drain screw)

I would agree maybe, but there are two of them, and you need only one for the drain plug, plus the drain plug ones are usually flat

A mistake in packaging ? 

Last year I bought a couple of drain plug crush washers that were of this style (i.e. not flat). I didn't end up using them because they didn't fit (inner diameter was too small). I think the dealer had the wrong size for the GS, but that the non-flat style can be used for these crush washers.