You are absolutely correct about the illicit FISA warrant and associated surveillance.
The Flynn case, on the other hand, is built on legitimate surveillance of Russian ambassador Sergey Kislyak. Flynn's communications with Kislyak had nothing to do with FISA warrants. There is no FISA warrant needed to intercept communications of a foreign diplomat.
That’s true, just taking issue with the notion that the Clinton campaign and the Obama government had any real “concern” over “Russian involvement”. They knew there wasn’t any and all they were trying to do was take ordinary situations and exaggerate them into something they were not: like the incoming NSA having an offhand talk with an ambassador, which is an ordinary event. And one that the FBI is almost never invited to or involved in.
And Flynn was fully aware that Kislyak was being tapped and probably also that his conversations would be
He just probably trusted that the US govt would not tap and unmask HIM as a potential enemy agent
You are missing the point that it is a federal crime to unmask an American citizen. Flynn is an American citizen yet no one has be held accountable for this. Also it is not against the law for an incoming Administration to talk to a Russian. In fact it is not against the law for anyone to do it.
As for the FISA warrant. If you intercept a conversation in this case Sergey Kislyak and you want to put him under surveillance you have to have a FISA warrant since this investigation was a counter Intel operation. Which means that they had the Trump Organization under surveillance with out a FISA warrant for months until they came up with the fake dossier and went to the FISA courts. Documents that have been released show this. It remained a counter Intel operation all the way through the appointment of Mueller. The DOJ does not handle Counter Intel Operation with a SC. For a counter Intel Operation you go to FISA for a criminal case you go to a regular federal Judge. Unlike the FISA judges it seems you have to prove your case to get a warrant.