Finish it the way it is - you have to really look to see what the problem is and I don't think your son is going to care. Put your last border on and get it quilted so he can use it. I have found that I need to square up each of my blocks to the right size before sewing them into strips. And I always pin where I want the edges to meet. It's so worth the extra time to do that. But, really, you've done an excellent job. I wouldn't worry about it.