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I have a 2007 F150 with the 4.2L. It was in an accident about 2 years ago. My insurance would not cover the repairs(long story) and I could not, at the time, afford to fix it. I since have began the long and tedious repair process. I have rebuilt the front end from the radiator support out. I had the transmission rebuilt. Mechanically speaking the truck suffered very minor damage (the clutch fan got bent and a blade broken off... Replaced it). The engine itself only has 39,000 miles on it.

Since I have gotten it back on the road it has had an engine shake when accelerating. Mainly first and second gear progression. Only natural it would run rough after sitting for two years, right? Well, I have since replaced the plugs, oil and filter, air filter, and all the fluids. Essentialy a complete tune up minus the PCV valve which my local auto parts stores don't have? Still shaking. I had the autozone guy hook up the computer to see if there was a coil issue, but the diagnosis had no misfires. I know the transmission is fine as I just got it back from a complete rebuild yesterday. I have checked the engine mounts and they are all fine.

I have a couple theories....

The emissions light is on in the dash. Could it be that the cat is clogged? Could an emission issue cause the engine to shake. There is some power loss or bogging in the lower gears, but not much.

Could a shaft or some thing be bent where the clutch fan mounts causing it to "wobble" and shake the engine? There is nothing obvious with the untrained eye.

Lastly, I have only ran about a quarter tank of fresh gas and fuel system cleaner through it thus far. Could I just be impatient and need to let it run for a while?

My main concern is that the Transmission folks were not sure what caused the transmission failure to begin with. I am scared to drive it too much with the thought that perhaps the engine shaking could have damaged the transmission (what else could it be it only has 38,000 miles on it?). The trans guys confirmed that its possible and recommended I get the truck tuned up immediately.

I really need to get this problem fixed and the truck back into fighting shape. If anybody out there has some ideas I would love to hear them.
 
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