I've repaired quite a few of these TDS5XX/6xx/7XX scopes so I can give you a few pointers.
First off, even though you have replaced all of the electrolytic caps make SURE that the acquisition board has been thoroughly cleaned. This means scrubbing the board with a toothbrush with a solution of degreaser such as Simple Green or Krud Kutter followed by a scrubbing with isopropyl alcohol. The TDS 500 and 600A series scopes were the absolute worst with the leaky caps, and once that electrolyte gets on the board it must be completely removed before it works again properly. After cleaning with Simple Green and IPA, I usually rinse the board with plain water and then dry the board thoroughly overnight with a fan running on it.
Once clean, you need to run SPC to re-iniitialize the calibration values in the scope - this will often clear up the "noise" you see in the plots you posted.
Good luck.