What's going on with this switched outlet wiring in the middle of a run?
Did not ultimately get a lot of help here, but I figured it out myself, so posting in case there are others who run into a similar situation.
The first key was figuring out how the wires in each box matched up. I connected D, the hot wire, first to A, then to B, which helped me figure out which two wires in the switch box they matched up to. C I knew was the neutral, so it was the third wire; whichever one I didn't hit by hooking D up to A &amp; B.
Then I essentially did this:


Knowing that D was the hot coming in and G was the hot going out, E was the neutral coming in and F was the neutral going out, I figured I had to connect the two of those
Realizing that I had a third wire, B, in my cable from the outlet to the switch, I determined I could use it as the second hot for the switch

So the top outlet is switched, the bottom is not, and I no longer have hots connected to neutrals, which to reiterate, is how I found it, not how I chose to wire it.