The water pump was dying, so I replaced it. I did the timing belt as well (may as well, it has to come off anyways).
I was VERY careful to line everything up when doing the timing belt. The cam sprockets and crank sprockets were all lined up dot-to-dot and the lines on the timing belt also lined up perfectly. I can't begin to fathom that I did it wrong.
Anyways, on first key after the big job, the engine started up and seemed lively. I noticed that it idled at around 1800rpm instead of around 1100 like usual. The RPM is always a bit high at idle now, not bad but noticeable. Being an automatic, it affects creep and downshift smoothness a bit when dropping to first for a red light.
It drives well and the power seems exactly the same. The water pump noises are now gone obviously.
I would almost think the knocking was always there and hidden by the pump noise, but the high idle makes me think there's an issue with the ECU or something.
Note that I can't set the timing absolutely because the balancer collar slipped, but I can tweak it slightly one way or the other.
Any ideas guys?