1a. I took the timely turn over of emails to the State Department as a separate issue. But I agree with you, Clinton does not look good on this. She apparently broke at least the spirit of the rules by not providing copies of her State Department emails to be archived until she was forced to do it.
2. Is it known that she provided classified documents to her lawyer? If so I was wrong and that has the potential to be somewhat bad to extremely bad for Clinton. I equivocated on how bad because there are different levels of classification and there is the issue of when what she supplied to her lawyer became classified.
3. I sort of agree with you I think, it looked bad but was probably not illegal. One of the reasons that this private email server scheme was stupid is exactly because of this issue. She needed to keep State Department emails, her foundation emails and private emails separate. If she didn't do that, reasonably enough, people were going to judge any ad hoc sort and deletion plan as suspicious and if you don't like Clinton it's pretty easy to judge it as criminal.
4. I kind of agree with the sentiment of your post but not the exact details. There is a lot of information that is not public yet. A reasonable criticism of Clinton is that her email server scheme unnecessarily put at risk sensitive documents. It seems unlikely that Clinton would not have communicated any sensitive information in her emails so I'm not a fan of the there-aren't-any-documents-that-were-classified-at-the-time-she-emailed-them defense. Still the extent to which she has a problem on this issue is not yet clear, I think.