Hi Erik,
First let me congratulate you on your dedication to this issue. I can see that you are doing your best to be as objective and as thorough as possible.
However, it's not entirely clear what image sizes you are comparing here. I get the impression that, for the purposes of comparison, you have interpolated both files to a whopping 200MB in 8 bit, and are comparing crops at the pixel level. Is this correct?
The native file size from the D3X in 8 bit mode is about 72MB and that from the S2 about 111MB.
The resolution of my 17" laptop is 1440x900 pixels. The screen is actually 330mm wide. That works out at 4.36 pixels per mm (1440/330) , or 109 ppi.
In order for my laptop to display the entire interpolated image from either the D3X or S2, my laptop screen, at its current resolution of 109 ppi, would need to be 2.3 metres x 1.64 metres, or 7' 6" x 5" 4".
When I examine your small crops of both images on my laptop, I do see fairly subtle differences in resolution. But I've seen greater differences when comparing different models of lenses, and sometimes even when comparing different copies of the same model of lens.
If such resolution differences that you've demonstrated were apparent in an A3+ size print, or even an A2 size print, or even a 24" x 36" print (of the entire image), then I might consider such differences as being significant.
But what you seem to be demonstrating are differences that would only be apparent in a 64" x 90" print, if one were to examine the detail in such prints from the same distance that one peers at one's computer monitor, ie. about 600mm or a couple of feet.
Assuming one were in a position to compare two 64"x90" prints on the wall, by the time you had walked from one print to the other, you would have forgotten the precise nature of those subtle resolution improvements in the S2 print. For all practical purposes the two prints would appear identical from a viewing distance that was sufficient to enable the viewing of both prints next to each other.
Do not apply for a job as a salesman for Leica .