1. It is a bit more complicated in this case. She did not just take copies of the email with her, she did not leave copies with state. It is analogous to taking the original of a document.
2. I'm not sure what you think isn't clear yet. Do you think her lawyer could have security clearance?
3. At issue is not that the vast majority that were turned over, but which ones were not and why. It comes down to how the selection process was done. If it was done by state or some impartial third party I would be OK with it, but having her own team select them should raise the suspicion of any skeptic.
4. What remains to be proven? They both took classified information outside of government control.