sounds like you also need to work on where in your hands you are taking the catch, if the ball is landing in and brusing the joints, the ball isn't going into your hands quite right. The ball should ideally be taken softly in the middle of the palm (small or large!).
If you have time practice throwing a golfball against a brick wall and trying to catch it right in the middle of your palms, then work on the higher catches.
Tough thing high catches, but it is all about confidence so once you get your technique right, you need to practice and practice...