Well, the answer to the right side is that the back of the fender needs to come up a little. Presto. That side is solved. No cutting or additional scratches involved.
The left side may not be so easy. Lifting the fender did help the hood gap but the fender to cowl fit still isn't right. After the first body guy showed me his "expertise", I wouldn't let him touch my truck again, no matter what I paid for his services. The money is gone and the damage is done. Lesson learned.
I may take your advice, Curt B, and try to remove a pie out of the inner-to-outer cowl panel and see if I can mash the end in a bit. My new body guy may flip when he sees he needs to fix some paint though. Oh well.
What's a little weld burn on a fresh coat of paint?! It'll give it character!