"Such systems are sometimes proposed as puzzles for evolutionary theory on the assumption that selection would have no function to act on until all components are in place."
I'm forced to wonder if this would have been considered a puzzle worth examining if it hadn't been for the likes of Behe and Dembski pointing out the (then-existing) gap in the theory and making an issue out of it. This paper came out in 2003. The previous study it referred to was done in 2000. Behe came out with Darwin's Black Box in 1996.
The issue here is that there are two objections against ID: One, that it's incorrect, which is a perfectly examinable assertion which I take no position on myself. The other is that it's "unscientific", which is simply an illogical objection. First of all, if ID is unscenitific, then so is the contrary position. It means the whole question of origins is an unscientific pursuit. Secondly, as the above example strongly suggests, it does result in scientific progress. It's not going to result in scientific regress. Why so many people react to it in such a paranoid fashion as though it's to be avoided like the plague, I'll never understand.
No, Darwin was aware of irreducible complexity and acknowledged the need to address it continually. The full case for irreducible complexity was made in 1802 by Paley in "Natural Theology". Origin of Species was a response to Paley.