The article I quoted says they confiscated the files containing the suspected classified documents. They weren’t going to have a sit-down and go through the files page by page while in premisses they’re searching. Was it a good search? No. Was it in good faith? Probably. It’s a pretty piss-poor plot to suppress freedom of the press when they seized documents, gave them back, and attracted a whole hell of a lot more publicity to the contents of the article than it would have gotten if it were published as normal. This isn’t a conspiracy, it was a mistake.
S/he makes just enough accurate points to indicate they they are probably sincere about the rest. 
What kind of paranoid nutjob would think that a 5am raid of their house with a warrant for unrelated charges ending up in the seizure of documents critical of the government might be founded in ulterior motives?
Jesus, pipe down and drink the kool-aid people.
The gov’t hasn’t been particularly shy about just subpoenaing journalists when they go after leakers. I don’t see any reason they 'd use a roundabout warrant for some other issue, especially since this way only works if they’re lucky enough that her notes on the story are stored in her house, are in files with documents marked classified, and even then such a plan seems as likely to backfire as anything else.
Plus the air marshal stories were eight years ago. It seems kinda implausible that someone woke up earlier this year and decided that they were going to track down the leakers for a story that was both almost a decade ago and wasn’t that big a deal even then.
The resisting arrest charge was the reason he couldn’t have guns, not the cause for the search. We don’t know what the cause given on the warrant is, but the Daily Caller article reference some stuff the guy put on Facebook and a complaint a few years ago that he was improperly discharging firearms.
Also, the guy did actually have guns in the house.
Anyhoo, I agree with Vercingetorix. I don’t think there’s really much going on here except that files released through FOIA should be more clearly marked as such.