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.
A. U.S. intelligence agency surveillance of Kislyak
B. U.S. intelligence agency surveillance of U.S. citizens
I'm not 100% certain about everything below, but I'd say I've got at least 95% of it straight. Here's my understanding of how the law works:
1. For Scenario A, there is no need for any warrant to conduct surveillance on Kislyak through wiretaps, intercepted communications, etc. He's a foreign national operating as a representative of a foreign government. Spying on people like him is exactly what intelligence agencies do -- constantly. They don't go and get a FISA warrant every time they want to intercept phone calls and text messages for one of these characters.
2. If Kislyak has a phone conversation with a U.S. citizen (Flynn, in this case) and the U.S. citizen is an innocent party to the call who is not suspected of any nefarious activities, then the U.S. citizen is considered an "incidental" contact and cannot be unmasked. Flynn's protections in this regard were null and void because his phone call with Kislyak was made from a foreign country (the Dominican Republic) while he was on vacation.
3. The illicit FISA warrants against the Trump Organization and various senior people in the campaign are related to Flynn only to the extent that Flynn was a campaign adviser who almost certainly had his conversations and electronic communications intercepted. That whole thing was a damned disgrace, but it is a completely separate issue from the legal process involving Flynn right now.
Flynn's legal troubles relate to Scenario A. The FISA abuse relates to Scenario B.