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@dmccandless One quick way to reduce the dataset would be to filter out any records where Store Point and Source_Store Point are the same. Sure it's a quick Zero distance calculation, but you know exactly what that one is. No need to do the work.
0.2s worth of a reduction in the workflow you provided using my machine, but every little bit may help here.
Do you need EVERY point or can you provide a maximum radius where if the distance is greater than a specified number it's not calculated?