From your description of the issue, I'm thinking that the hood may have had some tweaking when it was off the original truck. Maybe it wasn't stored correctly and got smooshed (highly technical P&B term

) a bit so that the sides are wider than they should be. Some judicious unsmooshing may be in order. With the cross support at the rear being fairly stout, it might be tough to do. Maybe a ratchet strap between the hood hinge mounting points, pulling them together?
Good luck