Good points. What about the 'stuttering' and "wiggling'? Neither a bad collet nor an out-of-tram condition should cause stuttering and wiggling. That's what leads me to agree with ger21, i.e., it looks like a R&P issue. I'm still thinking there may be a bind, maybe induced during homing, that is the underlying root cause. A bind could cause the symptoms described, and could result in lost steps, or a sort of hopping. Something as simple as the stepper drives not being tensioned enough could also be an issue - would seem like skipping (stuttering and wiggling) and could be present on one axis (Y) and not the other (X).
Gary