Im also suffering the same issue with large temperature spikes, also have a core xY and it only has the spike issue when x and y motors are moving , and not with the extruder or z axis motor,
If the OP's issue only exists in S3D (assuming the OP has rigorously tested that statement), then I don't see how it's a cable, EMI, or anything else hardware related since that should be software independent. Seems like a send/receive issue between S3D and the controller. I've had similar issues with custom builds. I think S3D is a great slicer, but I prefer other interfaces for controlling my printers. I usually slice with S3D, but control with Pronterface. I have fallen into the debugging rabbit hole too many times, and it's not worth it in my opinion if you can just control the printer with another interface and slice with S3D.