Welcome to the forums. Congrats on the new ride.
Can't help you with the headlight problem on the Gen II's, but I have seen a few people with the issue... so you're not alone.
And as far as the hood - that can't be right!!!! This is a brand new purchase? I'd be back at the dealer so fast demanding a resolution - don't wait. Start that ball rolling now. And you say you noticed this on other cars? I'm very interested to hear if other Gen II owners have this issue.
Sorry to hear about the problems, but glad to have you hear.