How did Felix's jerkass boss know who Bond was? At the time Bond is still just a relatively new agent and hardly someone who would be brought to the attention of the station chief for South America.
He might have known from the fiasco in the embassy from the last movie. I believe Bond's name was all over the media.
And yet this slipped past Greene?
Bond was MI6's man in the poker man, and Felix knew that fact. Perhaps the CIA knew who he was and let Felix know in case they needed to co-ordinate (possibly in a "we lost the game, let's team up and just flat-out kidnap the man"), and Felix's boss either knew who Bond was and it was a test for Felix's commitment, or knew Felix well enough to figure out he was lying and used some quick thinking to piece it together (MI6 just called him asking about a man, who just happens to tell him that he found someone snooping around outside his property, who Felix knows, so how many people working for MI6 does Felix know again?). As for Bond's name being all over the media, all the media reported on was that a British Agent killed a man in an embasy, and the only photos we see are ones taken from behind Bond where his face isn't visible.
How does gouging Bolivia on their utility bills count as a scheme worthy of a transnational conspiracy? Last I checked, Bolivia wasn't exactly the richest country on the block, even by South American standards. Also, starting the massive gouging immediately after getting the last of the land needed to control the bulk of their water supply not only tells the new leader who's responsible, but also what piece of territory he needs to retake to make the gouging end. If they'd slowly jacked up the price over a few years the general wouldn't have known how he'd gotten screwed. The choice of Bolivia is notable in that ten years before the movie was filmed, foreign companies had bought up the nation's water resources to jack up the prices, with the result of causing large scale riots. You'd think Quantum would have remembered that.