I have always simply ran the nVidia install script in full each time a new kernel is used. This is because the installer looks for a pre-compiled module and when it doesn't find one, it creates one.
When you run the installer and get a "Package not found" error, I would guess it is because of this:
(3) Erased installer "rm ./NVIDIA*run"
In my experiences, a fresh install of the nVidia drive is the best way to go.
Hope this helps