Under the light of a red sun, he is powerless and mortal, as are all Kryptonians. Under the light of a yellow sun, Krytonians are practically omnipotent.
The reason why kryptonite is so deadly to him is because it has RED sun radiation on it, from when Kryptons' red sun exploded. The red radiation slowly drains his powers, and since the red radiation is sapping his powers, it is causing intense pain because its red radiation, which makes Kryptonians mortal.