Thanks for the tips, everyone. "Framing" was exactly what I was looking for. Last night I was able to use it to manually focus my scope and get a V curve reading while I did it. The results were much better than I had been doing before. For people landing here from search engines:

If you want to manually focus your camera with Ekos, don't select a "Focuser" in your Ekos profile. When you start Ekos, INDI, and connect your devices, on the "Focus" module, you will see buttons for "Capture" and "Framing". "Capture" will capture a single frame for you to preview, and "Framing" will capture a continuous loop of frames. Click "Framing" and begin to adjust your scope's focus manually. The chart below will plot the V curve for your focus throughout. You should be able to achieve a relatively sharp focus. This is probably nowhere near as tight of a focus as you could get with a motorized focuser, but not bad either.

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