Your sensitivity due to previous damage is I think rather unusual, so not many others will have directly relevant experience. However I can say that when I started using the pump, due to the limited response of my penis it was quite frequent to experience the pain from my scrotum being sucked up by the pump. It needed trying the various alternative rubber seals and insert tubes provided with the pump to get the best solution, plus Andy62's trick of pulling the scrotum away from the pump opening.
Once I began getting a decent penile response, I was able to go back to the standard (larger) seal and tube.
Good luck!