Resolved, I think.
I mentioned that the engine in the car was a swap, and that I didn't do the swap. After tearing down 2 other engines in my local PullAPart, I found out the 1.9 only has 1 knock sensor.
The best explanation I can come up with is that the guy who did the swap carried over the other sensor from the swap engine and also connected the cable from the sensor that was on the original engine. There's a location up higher on the block where the sensor appears to fit, but that should actually just be left empty.
I swapped out the cable connection on the sensor strip, and (magic), my misfire codes cleared up. Who would have thought :-(
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