I don't have a hardtop but I do have a tonneau cover, which fits tightly over the folded hood. It fits exactly the same with the glass-windowed hood I now have as it did with the old plastic-windowed hood. Have you lubricated all of the pivot points in the hood frame? It might help. I give mine a tiny drop of 3-in-1 once a year at every pivot point and the hood operates beautifully.