Nothing is perfect and if you are looking for P E R F E C T you will kill yourself trying to acheive it. We are all trying for perfection, and that is not the same thing as PERFECT. I say let it go, put on the third border and stand back and admire your first quilt. Your son is not going to be looking for imperfections, he is going to be loving the quilt his mom made for him. Isn't that what is most important? The quilt is wonderful and the colors are great...you have done a beautiful job on the quilt.
Perhaps it was the folding that caused your problems. Are you squaring up each square as you complete it? Are you pressing each square before you square it up? These are steps that help me so much.