The D3 series is notorious for the shutter throwing oil, some of which eventually ends up on the filter over the sensor. When you stop all the way down oil tends to be a larger undefined gray area
rather than the smaller and more defined blackness of hairs, grit and other things sitting on the filter. If you do a wet cleaning and it still looks like you have those undefined gray blobs, it's probably oil. Unfortunately, they don't come off easily. You probably should have Nikon do the cleaning, as the amount of pressure and cleaning you have to use to remove it puts your filter at risk. Soapy cleaning liquids (e.g. Visible Dust's) seem to work better on oil than alcohols (Eclipse).