I don't believe those first two communications, as described, are actually illegal. I'm aware of the Logan Act, but believe there is no way it would be found valid or enforceable, particularly in this context.
Taken literally - which is the only way to take it and have it apply to Flynn - any time a private citizen expressses a wish or desire regarding what they'd like to see a foreign government do, that would be a violation. The reality is that happens on more than a daily basis. There are uncountable speeches, lectures, conferences, meetings, pronouncements, etc., in which private America citizens urge foreign countries to act in a certain way. Commentators routinely due that on TV, all the time.
Fuck, we've had private Americans do that consistently whenever hostages have been taken, even against the express wishes of the President.
Former President Carter essentially negotiated a nuke deal with North Korea, amd presented it to Clinton despite being asked not to do so.
Logan Act is toast.