@andy, have you given any thought to just removing the well circuit from the Sense readings entirely? You’ll lose the ability to track the pump usage as part of your overall numbers, but you’ll also remove it as a source of randomness in your usage signature and theoretically improve your detection performance.
If you have a traditional single-panel setup, you could run your pump circuit conductors through the Sense CTs alongside your main panel feeders, but in the opposite direction. This way, the current flow associated with the pump will cancel out as seen by the CTs. If your pump circuit conductors are small enough, this should work well.
Alternatively, depending on your panel configuration, you could locate your pump circuit upstream of the Sense CTs.