No, the 5.4 manifold can't be used on your 4.6. The 5.4 has a taller deck height, hence the ports are further apart on the 5.4. I don't think there is much reason to use a 5.4 intake though, because the stock PI intake works perfectly for a street engine with a 6000rpm rev limiter.
I'm not sure if anyone makes an adapter to run the 5.4, but it would be VERY difficult because the 5.4 manifold is much wider. I'm sure there are adapters to run a 4.6 intake on a 5.4 though.
Last point... does it matter if the intake is made of plastic or not? The only reasonable cause for a backfire is incorrectly used nitrous setups.