And the loose Y axis motor coupler as mentioned a few replies up. The update also caused an issue with the homing of the machine and loosing the Y-axis intermittently. Between the rapid movement in the corners (circles out of round), I reduced the cornering speed by 50% which reduced the jerking, tightened both couplers on Y. Reloaded the Ras-PI and have had no issues since.
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Also turns out the wrong Y motors were sent with the machine. 1F is sending the correct ones.
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