It's not clear why you want to exchange the 80-400 for the 70-200 lens although I am assuming that you want the extra speed from the smaller F ratio.
You do not say whether or not you used MLU with your tests? If not, then mirror slap could be an issue. You might say that at ~1/100" it should not be an issue as the problem zone is said to be ~1/15". But I was unable to obtain sharp exposures with a Nikon 200mm micro lens at 1/100" until I stuck a bean bag on top of the camera. MLU might have solved that.
Secondly, the light has changed from contrasty to flat, and that can affect the image quality, though the 200-400 lens should cope well with that by all accounts. However, it might still influence the results.
Lastly, you probably have heard that Nikon are introducing a 70-300mm F4-5.6 zoom, though that will probably be too slow for you if I have guessed rightly the reason for changing.
There is a test on
www.NikonLinks.com of the Nikon 80-200/2.8 AF 2-ring zoom with Tamron 1.4 and 2.0 teleconverters and comparisons to other lenses. By all accounts the lens is optically comparable to the VR version. Of course the problem really is what does the author mean when he uses the term excellent. One persons excellent can be another's useable. But he does compare to other lenses, so that gives some indication.
Leif