Three things:
1. Now, line up the eyes in these pictures and it will disprove your own point that the eye placement changed.
2. Look at the nostrils. Why are the nostrils of the production piece showing slightly more black (appearing bigger?)...simple, it is because the camera angle is very slightly lower than the camera angle in the proto pic.
3. For such a stickler for details, your lines are not precise enough. They are too thick, and you appear to be purposely lining them off of very slightly different areas of the images and claiming they are lined up.
You claim the red lines show where the sculpts don't match and your yellow lines show where they are correctly matched?
Your yellow chin line is slightly ON the chin of the proto, but slightly UNDER the chin of the production piece.
Your yellow ear line is slightly ON the ear of the proto, but slightly ABOVE the ear of the production piece.
Your yellow hairline at his slight widow's peak has the same problem, but this may be due more to paint application differences.