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My dad has a '99 250 5.4 auto 4x2. Last summer it started idling rough and wouldn't startup without some throttle input. It was an intermittent problem so he didn't want to mess with it until recently when it started getting worse. I gave it a throttle body cleaning with brake cleaner and a brush, and also took the IAC valve off and cleaned it and the ports. The truck idled better after this but acted like it had a miss that was barely detectable.
Just in the last couple weeks it has gotten much worse and he had a mechanic replace the IAC valve. Now when the truck is idling, it jumps between 700-1000 and the truck starts shaking pretty bad in a rythem. It goes away completely when you rev it up with the throttle some and seems to sound fine and have normal power above idle.
So far as I know, it's never had a basic tuneup (plugs, coils, pcv valves) with 160000+ miles. He's always been bad with maintainance. But it doesn't seem like that would cause it to only run bad at idle....