If your engine is still in the car you can still take measurements from the cowl and the inner fenders. You may still be able to bolt the hood on too.
There is one other thing you will need to consider if you're using an air intake system that will extend through the hood. In order to make sure that everything fits together properly you should mock up the tunnel ram, carbs, and air cleaner(s). Then lay some straight edges over the opening for the hood. Take measurements from the cowl and fenders to determine as closely as possible the location of whatever will be sticking through the hood. Transfer those measurements to the hood. You will have to cut for additional clearance but this should allow you to put the hood on the car. Most likely you still will be unable to close it though. When hoods open they do not lift straight up, - they move forward and back. So you will have to cut more for clearance as the hood moves. But after you have that initial hole cut and have the hood back on the car you can use a marker to indicate where the opening will need to be enlarged. Keep trimming but stay conservative until you can get the hood to open and close properly as it clears your engine.
The scoop hole can still be modified to facilitate any sealing options you may decide on or to allow for a bigger hole if you want to mount the scoop from the bottom. But at this point you will be sure that you won't have clearance issues later.
When we cut the hole in our Charger hood we had the hood on and off several times. I think we may have had to trim an additional 3 or 4 inches from the back of our opening to compensate for how much the hood moves as it opens. Our goal was to keep the hole as small as possible because there would be no scoop covering it, but we had to have adequate room for the engine to move around and hood to hinge. We didn't want it to look like we just butchered a hole in it. We would have liked to have had a smaller opening but we had to make sure that our linkage would clear too.
