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Hello,
My mother had a 1997 Ford expedition xlt, its 4.6L and is 4x4. I have done alot of work on it here lately, Replaced all the timing compontets, Plugs, wires, Had one head rebuilt, replaced Belt, belt tensioner, replaced a couple Injectors, replaced all the Lash adjusters. But heres my problem, when started at first it like knocks up in the throdle body, The noise is loud at first but once it gets a lil warm it pretty much goes away but if you listen hard it can still be heard. I had one person tell me that an oil passage on the cam cap my be clogged. But i am haveing trouble diagnosing this one.
Well first off, I would of put a 5.4 in it, but that's just personal....anyway, how many miles are on it? You should of rebuilt both heads, now your going to have inconsistant cylinder pressures with the newer better seated valves.
Now for the problem, I'm betting you have a lifter not staying pumped up and then it not holding pressure. I don't know if the 4.6 has a baffle on the manifold like the 5.4, but it could be a leak or crack on that also.
If the passage is plugged on the cam, you'll see the bluing on it when you pull that manifold. In anycase it appears the manifold has to come back off.
Matthew, sorry but when I read your post to my husband he said, uh oh, that doesn't sound good. If it makes a noise when you first start it then something has wore out. Good luck!