2004 F-150 XLT Check engine light on
 

Approx. 4 months ago I had the check engine light come on. My mechanic said the computer read-out shows that the cylinders are not firing on one side. He switched the coils from one side to another and reset the computer. He stated that if the check engine light comes back up and this time it's on the other side, then he knows is the coils and he will replace the coils on that side.
Now the first 15 minutes when I drive the truck, it s very hesitant and jerky and shakes like a leaf. After the engine warms up, it runs as good as new. Once I shifted into reverse and tapped on the gas, I heard a loud Beeep, all the lights came on in the dashboard and he engine died. I shifted into Park, restarted the engine and all was good.

I took it to the dealer and they claim there's something defective inside the engine and recommend to replace the engine. That doesn't make sense to me. If something was broken, would it not get worse and worse and not disappear after the engine warmed up? I don't notice any loss of performance or anything.

I am no expert but could it not be the coils like my mechanic says or a switch on the transmission that reports back and forth between the computer so that the truck knows in what gear to shift?

I think the dealer sees I am a woman, sees the truck is in mint condition and thinks I take good care of the it so I'll probably will just spring for a new engine.

What do you think? Right now I am thinking to take it for a second opinion to another Ford dealer.

First, I believe you are absolutely correct in getting a second opinion.
Also, there have been some problems with those engines, but in the event the second dealer provides the same advice, ask for a thorough explanation of what the problem is and why the engine needs to be replaced and if possible write it down. We would like to hear/see it and based on the explanation either agree or suggest something else.
Can you do that?
By the way what was your mechanic's opinion on this ?

Mechanics comment
 

My mechanic is an independent mechanic that AAA recommended. It's just cheaper to have a good mechanic that doesn't try to upsell you and strangles you with union wages.
He said that doesn't sound right to him. He went over all the things that could be wrong with an engine, from piston to shaft and he said none of this really makes sense with the symptoms I am experiencing. He recommended against to just blindly replacing an engine when they cannot even pinpoint where the problem is. He said they will replace the engine, I'll still have the problem and they will shrug their shoulders and say: "I'll guess then it wasn't the engine after all. Let's try something else". And he said it could be just some sensor or a solenoid, coils or such. He said if there as something with the engine, all the problems wouldn't stop after the engine has reached its operating temperatures.

The clue is that whatever it is , is affected by temperature. Usually a poor connection will show up with temperature changes. You might have your mechanic check the plugs on the PCM (powertrain control module). Some of them were affected by water intrusion where they plugged into the PCM. The result was corrosion at the contacts.

I took the truck for a second opinion to Theodore Robins Ford in Costa Mesa. They read error code P0012 which means variable camshaft timing over-retarded. All it took was a replacement of the solenoid, total was 472.04.