Vibration in the shifter is normal. It shouldn't be excessive, like if it's jumping all around then you have a problem. But a constant vibration is normal.

I understand you on the short shifter issue. I didn't notice a huge difference either when I changed mine out.

My brother has a prelude and I occasionally drive it. And I don't notice the vibrations as much in it either. Maybe they have softer bushings or it's just a different design.