'glass can be tough. First thing is to know sometimes you have to split the difference, adjust everywhere you can, and accept a little mismatch. Even the Shelbys had hood line issues.
However, if it's real bad, you'll likely have to work the hood if the door gaps are good and the engine compartment lines are square. If you still have a stock hood, it wouldn't be bad to adjust everything with that then remove it and fit the 'glass hood
I have had to cut, fill, shape etc, every fiberglass piece I have ever put on anything. It can be a pain, but the good thing is, once something is all the same color, assuming the gaps are straight, it will fool the eye a little, but you will always know it's there