In the picture it looks like you didn't paint the roof. What are you going to do to protect the metal from rusting under the vinyl?
I just noticed that too, You should paint the roof... I think that is the key thing to do to prevent rust under the vinyl...
At least paint it with a rust encapsulater like Rust Bullet or POR 15 - Ford left the insides of the cowl unpainted and we all know how that turned out