I think you're close in your first suggestion, but it's not so much that the lost prophet's words are unheeded so much at it is that his words are unappreciated, or not understood, especially at the time of their utterance.
Quite often, a lost prophet's contemporaries can't comprehend his message, so they don't recognize his brilliance; to many, he seems merely wayward and confused. Later on, though, people begin to recognize and appreciate his genius, and thus the label is bestowed as a belated compliment.
In the Economist article, the author is talking about conversations that foster and refine major ideas – whereas such conversations were once largely confined to university campuses, the online environment now allows more people to participate. But this wider audience is a mixed blessing: for every brilliant recluse there is a shallow curmudgeon.
The back-and-forth between bloggers resembles the informal chats, in university hallways and coffee rooms, that have always stimulated economic research, argues Paul Krugman, a Nobel-prizewinning economist who blogs at the New York Times. But moving the conversation online means that far more people can take part. Admittedly, for every lost prophet there is a crank who is simply lost.
In this case, the label lost prophet is not so much being bestowed belatedly by historians, but applied to one who has perhaps had the keen insights all along, but, until now, had never been granted a seat at the table. But, as the article implies, that next person pulling up a chair could be a keen savant – or could be a blustery know-it-all instead.
In this context runs counter to would mean the same as contradicts or goes against.
Counter here means against as in counter clockwise, counter argument, counter intuitive. To run counter to is to move against or oppose.
Best Answer
Here, the word "very" is used to put additional emphasis on the word it modifies: "first". It's a shorthand for saying
Or: