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My 96 T-Bird 4.6 came with a plastic manifold. After 6.5 years and around 90,000 miles, it blew out just behind the alternator. Ford knows about the problem and fixed mine for free. They replaced it with a plastic/aluminum combination maniforld. It's easy to identify because the coolant crossover behind the alternator is now made from aluminum.
Not all 5.4L intakes are composite. There are some old 5.4L NPI intakes that are aluminum. Also, the runner design may be different between the truck and the car, but with the proper toys, you can go so far as to put a 99 Mustang GT PI intake on the 4.6's that are NPI. It's about a 15 RWHP gain if I'm not mistaken(On a T-Bird anyways). I'm sure I just repeated a lot of well known information here.
I asked this question because I have a 97 Lincoln Town Car that has that plastic intake. So far it has held up but, it is always on your mind that this thing is going to crack, but when! Things like that usually happen when you need that aggravation the least.
My original manifold blew under a full throttle acceleration event. It never showed any problems up to that time. And there was no doubt where the leak was coming from. It gushes! When yours goes and you replace the manifold, make sure the spark plug areas are nice and dry or you will have one stumbling engine on your hands. My advice is, soft pedal the engine so as not to raise the pressure of the coolant, or pick your time and place and replace it. I understand the new manifold was standard on police cars and taxi cabs.
From what I understand, if you can make a bracket to mount the alternator on the engine block or a cylinder head, you reduce the risk of cracking the all composite intakes. Some say that the reason they break under WOT is because the alternator is making one heck of a strain on the intake. So, if you can mount that alternator on a more solid structure, it *should* keep it alive.
From what little I have read(which is mostly about cars), the all-aluminum intake saw the end of it's days in 95(for the 281) and in 96 the intakes convereted over to all composite. Someone please verify this info, and correct any errors. If what I have read has steered me towards the light, then I would guess that you maybe got a truck that had the intake replaced? I know that some of the 330's had an all aluminum intake for the NPI application(in 97) but when they converted over to composite on those, I don't know.
I've seen all plactic 5.4 intakes, but I've never seen an all plastic 4.6 truck intake manifold.
The below link shows a comparison to a '98 4.6 intake and an '03 Explorer PI intake. The top part which is mostly what you see when you open the hood is aluminum, but the bottom pieces that bolts on is plastic.