Some suggestions:
- Don't get too carried away with "independent" layers. Never have an independent layer with all children indepenedent for example (it makes no sense). In your case, for example, don't make Body independent. (Most of the others are fine).
- If you zoom out in rigging mode and click on the "Left Eye" and "Left Pupil" layers, you will see a yellow outline around your artwork... but the blue bounding box is really big. That is typically caused by some stray pixels in the layer. The yellow outline is where it tried to find the main artwork, but the blue box matters too. The eye I think is not moving because the "size" of the pupil is the same as the eyeball (both really big), confusing CH.
To fix it, what I do in Photoshop is to select the layer, use magic wand or similar to highlight the actual artwork you want, invert the selection (command-shift-I or something), then hit "Del" to delete everything else. This deletes any stray pixels. Do this for the eyeball and pupil layers (at least). You should see the yellow outline and blue outline afterwards the same size.
If the pupil does not move far enough, add a "Left Pupil Range" oval/circle as well and hide the layer. You can then make this oval bigger than what is visible, giving you more control over where the eye can move. I make it semi-transparent while testing, then hide the layer afterwards. (Remove the pupil range tags from the eyeballs.)
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