Unfortunately, it's not a loose connection issue. I bumped the Y motor up to 700, and even at that, it will miss a step, especially in infill jobs where the bed bounces rapidly around. I am using the same profiles in Cura that I did with the old board, and I did not have issues like this unless I ran it past 100mm/s, so I'm at a loss as what to do now.
I have hundreds of hours on this profile, or close variants of it with great results.
Also, is there a extruder calibration option or do I have to keep using the slicer for that?