Noise caused by the separate power supply of the sensor?
Most likely EMI is from DCDC common mode leakage and unbalanced sensors.  But a complete physical layout is critical.
With cable types.
To remedy CMRR connect Line gnd to 0V or use a cap for AC noise interfering with nyquist bandstop inside 2axis Accel.  Even though this defeats the opto isolation, it should still work.  You could run the RPM opto from 3.3V with the series R reduced for same current and try different GNd caps to Earth Gnd to block 50Hz but shunt RF and DCDc leakage noise.
Then add LC filters or Rc filter to 3V3 to mitigate if noise exists and make noise &lt;100uV into AC coupled 50 ohm scope terminated.
if it still exists use gnd shielding. Or CM choke to sensor LLC filter.
It would help if you defined all nearby noise generators.  Your noise could be above sampling rate or below with a thousand spikes in 30e6 samples.
I presume RPM is ok. Even though 24V is overkill for a 1.2V IR diode