I use to have similar problems before I started to stretch my balls.
My balls hung a little more than average and had about the same level of pain or discomfort during sex or jerking off.
Once I started to stretch, I notice the boys were able to withstand what was normally painful. Once it was apparent that they were starting to hang lower, I couldn't keep my hands of of them. I would spend more time playing with them, something I was never able to do before. Discovering this, I then began to push my boundaries around my fear hurting my balls. Currently the boys can withstand all the bouncing, squeezing, chewing or even punching that they are confronted with!
So thats what I recommend for you, start handling them more during sex, while watching T.V. or whenever it seems right! In time you will build up a tolerance to what was painful and begin to enjoy your very impressive balls!
Good luck!!