Bart, I would appreciate if you could expand on this. Much of my work is, if there is a such a thing, high end web based. I don't need huge megapixel resolution, I need really sharp and micro detailed smaller/medium size images.
Yes, your objective is becoming clearer now. The added number of pixels are not the real reason for the higher resolution though, although that can be achieved by down-sampling (but you seem to have some issues with that, which we can also solve). It also has to do with how dense the sensels are packed, and denser sampling will pull more resolution out of any lens.
Here's a google image search for pave diamond:
http://tinyurl.com/on9nna6
For those I'd assume that DOF restrictions are your main cause for loss of resolution, assuming that the entire object must be in focus. For such objects it is almost unavoidable to do focus stacking at the lens' best aperture. However, in the plane of best focus (which is much thinner than the DOF range), the previous sharpening observations still stand, i.e. aperture determines resolution and therefore the sharpening radius that's required to restore resolution. Focus magic or Topaz InFocus are dedicated deconvolution sharpening tools, and Topaz Detail also offers deconvolution, and other tools that address the different levels of detail.
Imagine one of those bracelets with a thousand diamonds and the client wanted every facet of every diamond distinct. it takes a high degree of resolving power even if it's ultimately not a high res image. (I fear the term resolution is getting confusing. I'm more talking about being able to discern (resolve) the finest lines through the lens and at the chip, not how many megapixels the resulting file yields.)
Here down-sampling can be your friend, not your enemy, so I wouldn't eliminate high MP cameras from your shortlist. Not only will the DOF limited resolution improve up to the limits of pixel size, but also (photon shot- and read-)noise will be reduced which would make sharpening easier because of a higher signal to noise in the image.
Now you make the point that an non AA chip will give better micro contrast at the outset, but that an AA chip may yield a sharper final by allowing more aggressive sharpening. Other than me buying/renting two cameras to test side by side (which I may ultimately do, but which two?) do you have examples or other means to illustrate which might serve me better?
It's hard to find direct comparisons, but it's a basic Digital Signal Processing (DSP) fact of life; discrete sampling introduces aliasing artifacts if there is finer detail than the sampling interval. Now in the case of the pavé seting of diamonds, there is an added complexity that may even help, and that's the DOF requirements. Since it will be hard to get sufficient DOF at the maximum resolution, the defocus will act as a kind of AA-filter. But that still leaves the in-focus edges susceptible for aliasing, so it remains a tricky approach (especially with a Bayer CFA that can lead to false color artifacts caused by aliasing).
The best comparison tool I've found so far is here (though I've not searched far and wide):
http://www.dpreview.com/previews/nikon-d810/9
And the Nikon d810 just looks better than the competition, though I haven't looked into the lenses and processing used.
From the specs the D810 certainly looks capable, and there are probably quite decent close-up or macro/micro lenses available. I have no experience with how well e.g. tethering works with the Nikons. My personal experience is mostly with Canons and they have good tethering capabilities, and lots of tools that support e.g. focus stacking like
Helicon Remote. The D810 is apparently also supported by Helicon Remote, so that leaves those options open.
Cheers,
Bart