A couple of thoughts:
While Nikkor 50mm f/2.8 is one of the better lenses and I use it myself (and very impressed by it), there is no guarantee that the one you have is undamaged. These days, we buy our equipment second hand and it is entirely possible someone may have took it apart to clean or otherwise caused some kind of damage. So I won't rule that out that your lens is bad. You might want to take it off your enlarger and inspect carefully for signs of neglect, damage, or contamination.
With that said...
I have no problem with my lens at f/4 to f/11. I have not tried outside of that range.
When I used "light weight" enlargers, I put my enlarger on a desk and I hang my timer on the wall so vibration from pushing the button does not transmit to the column. You might want to try it. Also.... is the sharpness of your image, the same all across your print? If not, your enlarger could be awfully out of alignment.