If you're referring to why Eli and Paul look the same, it's because they were twins - they were originally supposed to be played by different actors (Dano was cast as Paul), but then the actor portraying Eli quit, after Dano finished his filming for Paul. Anderson chose to recast Dano as Eli, but decided not to reshoot Paul's scenes with a different actor and just make the two characters twins.
And about the Kubrickian nods, Anderson originally was going to have the bowling alley painted white at the end as a "Clockwork Orange" reference, but then found out that someone was buying the mansion they were shooting in afterwards so decided against it - so yes, there's definitely some Kubrickian influence.
And about the last lines - with Daniel's last action, murdering Eli, he's finished. He will be arrested and lose everything he has, which is what he is personally referring to - that's what he means by the line. The underlying message is that the last of Daniel's sanity is finished - whatever sanity he held on to, by even the slimmest of threads, snapped, and he's psychologically finished. The entire movie is really about Plainview's slow descent from a successful, cunning businessman to an absolute madman, and the real question that it raises is - did greed *make* Plainview a madman, or was he always a madman, and merely waited so long to show it, his facade slowly disintegrating over time?
That's how I interpreted the film, anyway. I could be very off base.