Ok, now I am getting an idea of what we are working with. The pain seems to occur when you need to stop the momentum generated by the punch. Essentially the pain is occurring in the deceleration phase of the strike so breaking forces = braking force=deceleration, correct?
If so, I have a few thoughts:
1.) Shoulder pain with deceleration of the throwing motion is very common in sports. Often the rotator cuff muscles, usually supraspinatus and infraspinatus (the muscles above and below the spine of the scapula, just under the skin. If you stand behind someone and touch their shoulder blade you are touching these) get over worked/strained/injured trying to stop the internal rotation that accompanies end range of the throwing motion. Often damage to these muscles, even long term repetitive stress, can result in a build-up of scar tissue, hypertonicity (increased/too much muscle tension), and a lack of mobility. If the backs of your shoulders/your shoulder blades are tender you may want to get this checked out. If you think this may be happening at least use a foam roller on the muscles. Of course caveat emptor applies here. I am not your doctor. The above does not constitute medical advice.
2.) I am very familiar with strikes such as the 45 degree strike you describe. I have heard them referred to as bear swats. They can be wicked effective. However, I am very much against likening them to a baseball pitch, even though people far more qualified to expound on the subject seem to do so. The reason being, when you throw an object you are not planning on making contact with anything. You are also planning on releasing the object and following through with the throwing motion. So the mass/force that you must decelerate is less because you are minus the object thrown.
What I think you are doing in the strike you describe is swinging your hand through the target as though it was a hammer. If you were holding a cue ball and decided to brain me with it you might very well use the same mechanics as the 45 degree palm strike. You would not try to pitch the ball into my head, and forget to let it go. That would not yield the result you want, my fractured skull. Instead you would swing the ball through my temple.
So, if you miss the pad, or hit the pad, or miss my temple, or hit my temple just let the swing move through. Your arm will probably swing well across your body. You are likely moving forward. This is not the ideal position for defense, but that is the risk of the technique. Trying to abort the swing at its peak/ its heaviest is just setting you up for issues. Both orthopedically, and the fact that you may be in a compromised position longer trying to put the brakes on all that force rather than if you simply accepted the natural swinging motion and let it carry you. If I pull my head back at the last minute let the swing go and step into me. Make me pay for moving backwards.
It is my experience that most people, when they re-categorize a blow like this into a swing rather than a throw, reflexively tighten their muscles just a little, and that seems to make all the difference in the world. Now they donâ??t try to stop the punch short like jab, straight, or hook. Instead they let the swing happen. They also do not let their arm get so loose that the shock of hitting something creates issues.
3.) I consider the strike described in 2 to be a completely different animal than the swing/sloppy straight that I wrote about earlier. In this post we are talking about swinging the end of our arm (fist, palm, hand holding a cue ball,) into and through a target, like pounding a nail or hitting a golf ball. In the previous post the punch was a mechanism where we used the momentum of our body to injure. The distinction is with most punches I work on using mechanics to bleed less energy off/waste less energy in order to hit harder, so hit more correct to hit harder. In the 45 degree strike it is more like swing harder to hit harder.
Hope this helps.