I think this song is really about James asking god to heal him. I'm going to try to explain it with just the chorus, I'm probably completely wrong, but who cares.
"Can you heal what father's done?"
I think this is in reference to his father hurting him.
"Or fix this hole in mother's son?"
Asking god to fill the hole where his mother use to be.
"Can you heal the broken worlds within?"
He's asking god to heal his body, mind and soul.
"Can you strip away so we may start again?"
He asks god to give him strength to over come and start his life back up.
I think this song is really about James asking god to heal him. I'm going to try to explain it with just the chorus, I'm probably completely wrong, but who cares.
"Can you heal what father's done?" I think this is in reference to his father hurting him. "Or fix this hole in mother's son?" Asking god to fill the hole where his mother use to be. "Can you heal the broken worlds within?" He's asking god to heal his body, mind and soul. "Can you strip away so we may start again?" He asks god to give him strength to over come and start his life back up.