It's all about the unhealed wounds, missed opportunities of childhood/youth and gaining the maturity of learning we never will. We just have to learn to accept them.
1) The book is largely auto-biographrical. The main character shares the name of its author.
2) Recall that Jones's character of Terrance Mann is JD Salinger, author of Catcher in the Rye. A story stuck in youth if there ever was one. Kinsella has to bring Mann on the journey because it is only Mann who can see the world as a youth does, in wonder.
3) Doc's greatest wish is to play a full game of major league ball, his youthful endeavor. When he gets the chance to do so he willingly, knowingly, gives it up...to save a child.
Is there a point to childhood other than enjoying it while you have it, then learning to move on when it's your time to do so? Don't we all wish we can experience, for a fleeting moment at least, the youths we wish we had? It's this wish that is in conflict with the demands of adulthood; mortgage, crop yields, etc.
I don't think it's his dad's ghost he plays with at the end. It's the ghost of his own childhood.