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I have the same problem. It feels like I am driving over roadway rumble strips when I am going from 2nd to 3rd, and 3rd to 4th gear. ( is that upshifting or down?? I get confused about that).
Do you have an E4OD tranny??
From what I have seen here, I believe that the EEC module controls all shifting in the E4OD, and I am also getting codes and a check engine light. I just did an engine change, and worry about what I may have done to my Torque convertor. I went thru 11 pages of this forum yesterday, and saw plenty on the problem about poor shifting. Try reading thru here deeper into the past posts you may pick up a couple of good clues.