I only recently learned about this and promptly discovered it in my own car, but check the lip on the underside of the hood for rust bubbling up under the paint. It's a very common factory defect.
Also, there is another defect regarding the fuel pump. After spending an extended period of time cruising at highway speeds, air bubbles build up around the fuel pickup and cause the car to "lunge" the first time you accelerate from a stop, like pulling away from a highway exit ramp. It's intermittent and is fixed by replacing the fuel pump, which is actually pretty easy. It isn't even worth it to me to fix until I need to upgrade my fuel system.
These cars have a possible design flaw in the gas tank filler neck, too. Some gas stations have pumps that for some reason don't like to work properly in these cars. They "click" as if the tank is full, shutting off fuel flow every couple cents worth of gas. The easy fix is to rotate the fuel pump nozzle upside down. Fuel flows freely and doesn't leak or burst out once the tank is actually full.
The '05 to early '08 4.6 engines have poorly designed factory spark plugs that easily snap off inside the cylinder head. Unless you know it's a later model one-piece design, either use a special tool made just for this purpose, or take it to a shop to have plugs changed.
I can't speak for the manual transmissions or clutches because I've never owned one. I very rarely hear about problems, though. When I do, it's worn synchros or something on a 125k or higher engine.
Other than that, I've encountered no problem with my auto '06 except it's at 58,000 miles and is developing a lot of vibrations and rattles coming from the car (of course, this could be due to the fact that it has long tubes, an x-pipe, muffler deletes and is ridiculously loud).
In stock form, I was getting 30 to 32 mpg on the highway with the factory 3.31 gears with cruise control set at 60. Adding camshafts, long tube headers, an x-pipe with catalytic converters, a larger air intake, and a Brenspeed tune, it dropped to about 28 mpg. A high rise intake manifold, heads, throttle body, and 3000 RPM stall speed torque converter dropped it to about 26 mpg highway and 14 mpg city driving conditions. Not bad for an eight year old, 425 horsepower engine that rips the tires off.
What mods have been done? Has the car been tuned?
