Well first of all remember and accept the fact that a repro or aftermarket panel is going to be "Similar to original, can be used if nothing else is available" but it will NOT be "exactly as original" like it says in the catalog.
First off, on that hinge being "down all the way" are you ROTATING the hinge back or simply pushing it down? Pushing the hinge down will NOT get the hood down as low as it will go, not even close.
You need to ROTATE the hinge down, lifting the front as far as it will go and lowering the back as far as it will go is how you get the back of the hood down as far as it will go. Pushing the hinges straight down only gets the hood about half as far as it will go.
Here is the "Basics of Basics" to panel alignment. (CLICK HERE)
If the hinge won't bring it down all the way you can shim it down too, yes shim it DOWN. Putting shims between the hood and the hinge at the front bolt (closest to the front of the car) will LOWER the back of the hood. It's doing the same thing as rotating the hinge back.