Scott,
Are you using repop sheet metal and or hood hinges? I recently put a repop hood and front right fender with stock hood hinges on a 69 Chevelle and faced a similar problem. I could get the sheet metal to line up decently, but the gap between the header panel and hood was about 3/8" TO 1/2". With a little bit of hood movement toward the front and a different header panel (GM), all the gaps closed up nicely, but the hood is still tough to close. The hood latch, upper and lower are all lined up well, but it still requires quite a bit of effort to get the hood to latch.
The other thing I noticed is that when closing the hood and the latch catches the first detent, the driver's side of the hood is about 1/2" above the driver's fender (which is a GM fender), while the passenger side is still up about 1 1/2". So the hood isn't coming down evenly. I also noticed that the hood hinge on the pass side requires that the front-hinge-to-body hole be fully adjusted down (as low as the front hinge hole allows, not normal in my opinion).
So if I was to guess without measuring, I'd say the repop fender hinge mounting holes are probably in the wrong position compared to a GM fender and that the hood does not close evenly, which requires extra force to overcome the torquing of the hood.
This weekend, I'm going to put a GM fender back on the passenger side to see if that solves the hard-to-close hood problem. The stock hood and fender combo had the hood lined up nicely and was easy to close. So the issue to me is with the reproduction parts.
Hopefully some of this info will help. I'd be curious to see if anyone else has been down this road too.
Woj.