Dear radders,
No experience with 2.0 liter manual diesels, but experience on Cummins diesels and high horsepower powerplants.
Vibrations from a diesel engine transmitting all the way through the transmission and shift knob are frequent. Many owners have to install aftermarket polyurethane engine mounts. These are far superior to the standard rubber mounts provided by Hyundai and most original equipment manufacturers. Your solution has to start with better motor mounts, and maybe require transmission mounts. Here is one mount source for information only- I have not bought from them personally so I am not shilling for them.
http://www.energysuspension.com/pages/motmtins.htmlByron