1. I analyzed 18 USC 793(f) over in the Clinton thread- long story short, for this to apply there has to be some act of removal of information from the proper place of custody, or delivery of information in violation of trust, through gross negligence.
I don't see what the act of removal/delivery of information from a proper place of custody would be here. I don't think it makes it unlawful to store classified information on personal email unless you're the one who directed (or through gross negligence allowed) a particular piece of information to be removed from a proper place of custody and stored there. And then there's also the question of whether something can constitute "gross negligence" when one's predecessors did the same thing. To me this looks like a stretch, but I know there are a few lawyers who have cited this as a possible grounds for indictment.
BTW the provision itself seems to be targeting people who do things like walking out of the Pentagon with maps and whatnot, not violations of recordkeeping and electronic communications guidelines. You can look for yourself
here and see if you think anything Clinton did can be captured by the provision.
2. Those are regulatory guidelines. To my knowledge there's no criminal penalties for alleged violations of those guidelines, and thus no possibility of indictment for their violation. But maybe someone else knows how this could constitute a criminal act?
3. I'm not aware of any criminal penalties for violations of FOIA (which I also believe applies to agencies, not individuals).