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Jonathan: Clark! Come on, son. The cow's aren't gonna feed themselves.
What, you have a late night? Tired from a long night?

Clark: I was helping Lana. To her credit, (as far as she's concerned?) she's not gonna let the whole
body part incident delay the opening of the Talon.

Jonathan: Well, that's what happens when you get into business with somebody like Lex Luthor.

Clark: Well, if it wasn't for Lex, the Talon would be a parking garage.

Jonathan: Son, he casts a very, very long shadow. (He's dangerous?)
I just want to make sure that none of you kids get hurt. That's all.

Clark: The past is in the past. The best we can do is look to the future. Does he refer to Lex?
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What, you have a late night? Tired from a long night?
Yes, to "have a late night" means to stay awake late into the night and usually implies that the subject is therefore tired.
I was helping Lana. To her credit, (as far as she's concerned?) she's not gonna let the whole
body part incident delay the opening of the Talon.
No, "to someone's credit" is minor praise. It's often used in an attempt to positively recognize someone in spite of a negative situation. In this case Clark is praising Lana for continuing with "the opening of the Talon" despite whatever trouble was caused by the "body part incident".
Son, he casts a very, very long shadow. (He's dangerous?)
"To cast a long shadow" is an idiom meaning that the subject has a lot of influence in a variety of areas. It does not explicitly mean that Lex Luthor is dangerous, only that he is powerful. However, the subtext is clearly that Jonathan Kent does not trust Luthor.
The past is in the past. The best we can do is look to the future. Does he refer to Lex?
It would seem that he is not referring specifically to Lex Luthor, rather just trying to be optimistic. However (assuming this is all taken from the television series Smallville) the audience is expected to know that one day Lex Luthor will be Superman's main antagonist, and thus the comment is meant to foreshadow. In that sense it does refer implicitly to what Lex Luthor will become.

Comments  
Thanks, YoungCalifornian!