It was the drain bolt on the EGR cooler that was leaking a couple of drops. As I said, very small leak, and it never introduced air into the system.
So, I tightened that MFer down and it stopped leaking.

I used a torque wrench to tighten it during my rebuild, and it seems to have loosened as it heat cycled. Next time I'll use a little RTV on the threads to prevent something like this.
Water level stays full now. I also rerouted my overfill hose so that it stays level, which should allow the system to draw more coolant from the overflow container. The damn container is on the other side of the engine compartment in the MR2.