The "self-defeating" claim you mention is Alvin Plantinga's evolutionary argument against naturalism. A number of mostly satisfying responses are listed on the wikipedia page. A brief search on LessWrong suggests that the EAAN hasn't been thoroughly critiqued here.

I suggest that you return to the Sequences, aggressively skipping the quantum stuff, until you've convinced yourself (and can convince others) that there's not much use worrying that evolution gave us a great faculty of instrumental rationality and a separate defective system of epistemic rationality. Such a situation has a vanishingly small probability and if it's true, there's not much to be done about it.