I thought you might be in for a surprise Lee
All of those that are clearly visible in your first image are on the CCD cover. You can tell by the size of them.
Don't worry about it, flats will remove them with np at all. Cleaning filters is one thing, they are easily replaced if you scratch them but the glass cover on a CCD is another story. Be very careful cleaning them. The suggestion I was given when considering cleaning my CCD cover was "Dont!!" unless it is really bad. Have a look at my SBIG thread and check out Dennis' SBIG flat.
and the dust mote on mine. The size of mine indicates to me that mine is under the class cover of the face plate. The actual CCD cover looks pretty good on mine.