Hi Paul,
Good to see you are working on improving your workflow. I was using PSE7 until December 2015 when I changed to PSE14. My reason for upgrading was to run some 64-bit third party plug-ins (PSE7 only supported 32-bit processing). I don't think I gained any other features that I regularly use for processing bird images that I could not do with PSE7. Jill recently upgraded from PSE11 to PSE15 when she bought a new computer. She has just confirmed that there are no new capabilities in PSE15 that she finds useful for processing bird images. The big selling feature of PSE14/15 is the facial recognition algorithm that is no doubt useful for some users but we disabled this capability as it automatically started working on our bird catalogues looking for new faces whenever we started up our computers.
I use Canon DPP for RAW adjustment and conversion and I do not have first-hand experience with Nikon Capture NX-D, apart from looking at it on the Nikon website. I believe it produces clean, low-noise RAW conversions which is a good start. Many different demosaic, noise reduction and sharpening algorithms are used to convert RAW files and there are noticeable differences in the resulting image quality. You should output 16-bit RGB from Capture NX-D to PSE for further adjustment. PSE has a limited capability for adjusting 16-bit files but it is enough to fine tune the lighting, colour, and make selections that enable you to work separately on the bird, the background and selected areas. To use the clone stamp and layers you need to convert to an 8-bit TIFF. Do the final downsize and output sharpening on the 8-bit TIFF and then convert and save as a JPEG. Do not manipulate the JPEG in any way as you will then need to save it again with a possible loss of image quality due to JPEG compression.
Hope this is useful, best wishes,
Ian