I have the exact same size machine with exact same problems. Performed all the same trouble shooting steps. My worst jitter happens on the x axis more then the Y.
My microstepping is 1/32 i think, all the jumpers on the ramps installed and DRV8825 drivers. Should we change that to 1/8 (jumpers 1 and 2 only, steps/mm = 50)?
My conclusion up to this point is the rails must be flexing on the tiny pits in the EMT conduit causing it to bounce back as it rolls. My solution very soon will be to reprint the entire thing and upgrade to 1″ stainless rails.