With the car running, and in neutral, if you only push the clutch in, does this affect the vibrations? If you then put it in gear, is it hard to put into First? With the <acronym title="transmission">trans
</acronym> in neutral and the clutch out, the input shaft is turning at the same rate as then engine. If you then push in the clutch, it is still rotating. Only after you put it in gear does that input shaft stop rotating (assuming you have tight tolerances on the clutch). With it now in gear, and the clutch to the floor, does your vibration decrease?
If it does, I'd wager you have a bad bearing on the input shaft.
At the least, you may have to drop the <acronym title="transmission">trans
</acronym> to verify they installed the clutch right. At worst, you are looking at a rebuild, but you may get lucky and only need to replace the input shaft bearing, but don't count on that.