Maybe this 6VE1 really isn't very smooth. I saw another 3.5L motor today. I went back/forth between both motors. They had (close) to the same vibration/harmonics around 2500rpms. Both smoothed out between 3500-4000rpms though one motor was noticeably smoother than the other. (Not a lot, just noticeable.)
Maybe this really is a combination of the motor's "character" -- plus a bit of mount vibration. It might also be that one needs plugs and/or injector cleaning to recover maximum smoothness.
Has anyone ever looked into installing new mounts and/or trying the heater hose trick relayed by Jerry?