So the tracking system is working, but it's just not accurate enough at this point. I've ordered a third sensor and I'm going to lengthen the tubes that allow the light to hit the sensors. I believe I'm currently getting too much light in the tubes even when it's not pointed at the sun. Lengthening the tubes should help that.
The shielded extension wires for the sensors are out of stock so it may be a week or two until I receive the parts.