Joe, I believe you need to be more specific on your question. The answers you get will be based on whether you are viewing your images in Nikon software or through Adobe software.
All of the in-camera settings are applied to an image when viewed in Nikon View NX2 or Capture. It will look exactly like the jpg if you did a Raw + JPG. (A TIF file converted from the RAW file in View or Capture could be saved as 16 bit, while the JPG will be only 8 bit, so even though they might look the same, the 16 bit image would have a lot more data.)
In Adobe products, ACR only initially honors the White Balance settings. Active D-Lighting gets ignored. ACR will apply its own presets which may not look much like the same RAW file opened in View or Capture.
ISO, focus, shake, and EV are part of the initial settings at the time of capture and will affect the image.
I am sure someone will correct me if any part of this is incorrect.