Looking at the scans, I see 24 times (later in the scan even tighter) a 10ns or 20ns pulse after the “lower” encoder sees a line. I don;t think that that is noise as there are times when these spikes do not show, plus they are evenly distributed, and lastly, assuming 10ns is 0 and 20s is 1, give a very simple binary encoding without needing an external clock source.
Do you have an idea what the remaining signals are.
BTW: it’s very nice to see the acceleration and deceleration in the light sensor sampling 😉