Since I think you're referring to the metal portion here, I'd carefully measure
both and compare them. If your replacement one varies from the oem one, then you know who the culprit is and can make changes accordingly. But, if they measure the same, then it sounds like you may need to slip a jack in to push up the edge of the roof, as either the roof or cowl is to close to each other. Measure the windshield opening as well; that'll help eliminate variables. Good luck.