Yep, that shell holder is generally the culprit. Briman on here took his spring out of the ram and lets his shell holder float. Worked well for me too. I can't say I can achieve 90% less than .002, but I do something simular I bounce my bullet/brass while seating. I will raise the ram right to where it wants to push then drop back down, it will center my brass. I get do get consistent less than 0.003 and .004" this way.

Sounds like you have taken it to a whole new level. I don't blame ya for comp shooting. Everything is everything there.