Subject Matter Jurisdiction is the one affirmative defense you're not required to raise. All others, if you fail to raise them in the answer, they're not available later. Personal jurisdiction objections can be waived, but not subject matter.
Responding to allegations is different from an affirmative defense. The defendant has two ways to win: failure to prove, and affirmative defense. Note that "failure to state a claim" is not just 12(b)(6): it can also be a kind of affirmative defense.
Rule 8 (and somewhat Rule 12) list the affirmative defenses. But this isn't necessarily an exhaustive list: you can add things in that don't conform 100%. Lists of defenses tend to be very inclusive it order to avoid accidentally waiving them.
Read the paragraphs in the complaint carefully: make sure you deny things worth denying (see, e.g., ¶ 1 in the Jackson v. Long complaint).
Note that complaints will have some things that can neither be affirmed nor denied (assertions of law, e.g., or statements like "plaintiff brings this lawsuit").
See 11(b)(4): denials of factual contentions must be warranted on the evidence. When you file your answer in court, you are asserting that your denials are either warranted on the evidence, or that you don't have enough information to believe them to be true. Basically, you can't deny things you know to be true. On the other hand, the more the plaintiff characterizes the facts, the more wiggle room the defendant has for denial.
Responding to ¶ 22. You'd want to interview your clients, at a minimum, and do enough investigation to figure out what you can deny.
Plaintiffs tend not to tell their stories in answers: just go paragraph by paragraph, and if there are grounds for disagreement, just deny.
I. QP1 I. BA1 II. QP2 II. BA2 Discussion Overview (has things that are common to both) Deal with QP1 Deal with QP2