This article assumes you are using a finger-tip drilled ball.
Assuming the span is long, it will strain the tendons in your fingers. Over a period of time, they become sore and it starts to hurt. Once this is corrected, its probably going to take a while for them to heal.. (not likely to instantly feel better, but over time it should).
If the span is long, the ball will likely need to be redrilled. The easiest way would be to plug the thumb and move it. Its likely that you span would only be off a fraction of an inch. Adjusting it this small of an amount should produce any noticible effect on you layout. You may, however, throw the ball a little differently..
Definitely go back and get your span checked (or just get your ball, put your thumb all the way into the hole, and lay your fingers overtop of the grips/holes... if the edge is close to your first crease, then its long.. if its near the middle between your first and second crease, you are close. You can also take it into your shop to have it checked...
Good luck,
S^2
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