Question: Who kills the informant on the boat? How is Verbal outside the boat and also supposed to be the villain who's killed everyone?
Answer: Keyser Soze killed the informant, Verbal was telling the cop his version of what happened to the cop and the movie going audience, to misdirect everyone. Confusing everyone until the revelation at the end of the movie.
Question: At the beginning of the movie, we see everyone getting picked up by the police for the lineup. Everyone except for Verbal. Given that he had the power to orchestrate the lineup, did he get picked up as Verbal, or did he get there some other way?
Answer: Verbal is telling the story to Agent Kujon and makes it up as he goes based on things he sees around the room. Verbal Kint is a master manipulator, so to believe anything he says is ridiculous. The entire story is made up, as he tells it using various bits of truth and things he can see in front of him, which help him to remember his lies. That there even was a lineup would need to be verified to know for sure. The only fact of the story is that the ship burned and all but one witness and Kint are dead. Everything else is speculation based on the word of a known criminal and apparent habitual liar.
Question: Redfoot is the whole reason they ended up in LA (he was the fence), and the reason they got connected to Kobayashi through the attack on the drug dealer. So if he's just a made-up part of Verbal's story, how did they end up in LA, and how did they end up connected to Kobayashi?
Answer: The fence did exist, he just gave him a fake name. His real name wasn't Redfoot.
Question: If the entire movie was the depiction of the ingenious and elaborate planning of Keyser Soze to kill the one man who could positively identify him, then what was the point of this movie? I mean now everyone knows what he looks like since they have his sketch.
Answer: The point of the movie is entertainment, and the twist ending provides that. Within the movie, Soze doesn't care that everyone will know what he looks like any more.
Answer: Basically, the actors were improvising their answers, and their inflection, and kept trying to make each other laugh. Director Bryan Singer was angry at first, but eventually decided it fit their characters and their disregard/disdain for authority, and so used the takes in which they were cracking up. In this particular moment, they were laughing at the beginning of del Toro's part because, apparently, he had just broken wind.