You've probably thought of this, but can you raise the fender up a bit and then tweak the hood to match?
I've heard a lot of people have trouble lining things up if any part is a repro. They just don't quite fit right all the time.
If you have a factory assembly manual it says what the gaps should be from the factory (and the tolerance). I'm going from memory, but I remember something about the hood being a little high to start with and then getting to flush as it gets closer to the front. 1/4" sounds like too much though. I can post the picture later if you need.
I should say that it looks real nice from here already!