Updating as I have a solution to my particular problem. The issue lies in a distinction between the different versions of the common YHDC clamp sensor.
Most low-amp sensors with the model number SCT-013-xxx come with a built-in burden resistor (SCT-013-030, SCT-013-050). However, the 100A version of this sensor, SCT-013-000, does NOT include a burden resistor!
I had removed the resistor on the bottom-right of my circuit board as I believed the sensor I connected was a voltage-output type. However, as can be seen in this documentation, the 100A SCT-013-000 is of a current output type (with a turn ratio of 100A:50mA, or 2000:1).
I simply moved the sensor to the screw terminals above which still had a burden resistor, re-calibrated, and now everything is working fine.
I learned a lot about current sensing and wanted to share some helpful resources I came across in my hunt for a solution:
Resources on selecting a proper burden resistor
For reference, I am currently using 10ohm burden resistors on all three active inputs. Per the calculator, a 100A sensor in a 3.3V system with a turn ratio of 2000:1 (SCT-013-000) should use a burden resistor of 23 ohms for maximum accuracy. A 100A sensor in a 3.3V system with a turn ratio of 1000:1 (PZCT-02) should use a burden resistor of 12 ohms. However, resistors are not always commonly available at these resistances.
Per the first link above, the burden resistor should be the “smaller value, or the maximum load current will create a voltage higher than AREF”. Therefore, the 10 ohm burden resistors are ideal for the PZCT-02 CT sensors, but this value is a little low for the SCT-013-000 and this could lead to accuracy issues. In my testing and for my purposes, this is not of concern, however I could change the SCT’s burden resistor to a 22 ohm.