If I use the Samurai's Challenge ability against an opponent (−2 AC except for attacks from my target), and use lunge to attack them (−2 AC until my next turn), do these two penalties stack for a total of −4 to my AC against attacks from other opponents?
Yes, they stack. These are untyped penalties, which always stack with each other.
The only modifiers1 that don't stack are typed modifiers when the type matches, in which case only the largest is used.
It's a common house rule / misunderstanding that penalties are special and always stack regardless of type. However, other parts of the rules themselves assume that typed penalties don't stack, clarifying the issue:
Usually, a bonus has a type that indicates how the spell grants the bonus. The important aspect of bonus types is that two bonuses of the same type don't generally stack. With the exception of dodge bonuses, most circumstance bonuses, and racial bonuses, only the better bonus of a given type works. The same principle applies to penalties — a character taking two or more penalties of the same type applies only the worst one, although most penalties have no type and thus always stack.