Shouldn't need to swap hoods to keep from breaking your corners. Your problem can be fixed with some adjustment. Quite frankly, you're going to just have to "tweak" these area's until everything lines up. Ford quality control throughout the '80's, '90's and into the mid '00's was shall we say....lacking. These cars on their best day were less than perfect. No two edges were alike. Loosen some bolts, shift stuff around, bend an edge here, tweak a corner there.....that'll get ya back into shape.
The fact that your current hood doesn't line up properly already tells me that it, or some other part of your front facia, fender, etc is A) out of adjustment, or B) the car at some point has been "tagged" in the front end, knocking it out of shape and needs correcting.
Also keep in mind, your aftermarket clear corners may not be built to the same spec as the OE lights. Compare the two side by side and see where the differences are. The results may surprise you.