I apologize if this seems like a question with an obvious answer, but it's been awhile since I've played a dueling card game so I want to make sure I'm reading the rules correctly.

When a defender with Counterstrike is declared as a defender, it immediately assigns and applies damage to an attacking unit. Assuming this is enough to kill the attacking unit, this takes place before normal combat damage assignment and as such that attacker does not contribute to the damage pool, correct? Thanks!

Yes, that is correct!

Yep. Also note: a unit with counterstrike can only assign its counterstrike to one unit, so unless you have multiple counterstrikers you only get to hit one. It's also uncancellable damage, so it will hit through toughness etc.

Counterstrike is or isn't combat damage? Never really thought about it before, but if you could boost and get CS to Juvenile Wyvern (if CS is combat damage)...