I guess the first question is how is the histogram. Is it showing underexposure but being bunched up to the left? When you shoot the custom white balance are you setting the exposure for that or taking the meter reading?
Here are my suggestions.
First Aperture priority or shutter priority should only be used in fast moving situations. For Stock Photos you should be thinking manual all the time because of the control.
With the camera in manual take a shot of your gray target and check the histogram in the camera. It should have a spike in the center of the histogram. If it is off then you need to make adjustments in the camera. I do not shoot Nikon but I know that Canon has an adjustment that can change the bracket of the exposure. It could be the same for Nikon. Try to get the camera neutral for exposure and close to your hand held meter.
Also are you shoot RAW +
? Since you are processing your images in ACR this is really not needed for two reasons. First
it waste space on the card and second you are going to do post processing in ACR anyway so just do the post and then go to Tools>Photoshop>Image Processor to make the jpegs. It works in the background from Bridge and the jpegs are now just like the better RAW images.
As to your question of how the images are out of the camera as to size and bit depth, yes they are 16 bit but if your final output is set up for 8 bit at the bottom of ACR you will see these readings. I would not worry about this unless you have some advance Photoshop training where you do some post processing in 16 Bit. With most of your processing being done in ACR there is less need for 16 bit processing in Photoshop but you can change the output image if needed.
Email me if you have more questions.