I believe the problem is you need to use the --swapxy flag in csparc2star.py for particles extracted in cryosparc. I often do a quick test of the coordinates by extracting a small subset of particles (1k) in relion based on the homo-ref star file from csparc2star, then take these to 2D class.
More on this here, just ignore my comments on flipping an axis as I was mistaken.
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