Ryan,
You have a beautiful jeep there, I think I would be tempted to put the hood back on as good as you can. And then I would take the whole jeep over to the guy who did the work and politely ask him if he could help you get the hood aligned/installed correctly. With a masterpiece like that, he is going to want to show off his work with pride, not have someone say " nice jeep, what happened to the hood". I'm going to guess he will work extra hard to make sure that his name is properly reflected in the hood fit up.
My 2 centavos