Thanks for all the informative comments, they are appreciated. These lead me to ask a few more questions.
The NEF images were uploaded by copying with Explorer and they were opened in Photoshop. Am I correct that with this process no in-camera sharpening setting would be applied automatically when the image is opened?
Does a low contrast subject combined with an f/7.1 or f/8 lens opening (a bit below wide open on a f/2.8 with a TC-20) challenge auto-focus on Nikon DSLRs? And might that provide an especial challenge for the D7000 or can I forget about this?
I'm a little surprised at the suggestion to not use Auto WB. The colors that I have been getting match nature pretty closely as to warmth/coolness (as viewed on a color calibrated monitor). What problems does Auto WB introduce?