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I don't disagree with any of the above, as I experienced almost the same symptoms as well as hard shifting 1-2,2-3,3-2,and 2-1.
Before anything else and by far the cheapest, find an independant repair shop and have them run the 3 steps of SMG teach-in and adaptation. My car drives extremely smoothly with no clunking or hesitation after reteaching the "H-pattern". I am mentally preparing for the clutch swap (2006 at 63K miles), but couldn't be happier with the SMG right now. Takes 30 min, so you're looking at 1 hour of labor.
May not be the answer, but certainly cheaper than a clutch if it works.