This is for a 2001 F250 w/5.4L
It started with the rough idle syndrome one day, so I figured I had a shot coil at approx 40000 mi. I bought a new coil and started to take apart the one I thought would be faulty. I thought it was the pass side, farthest back. I also decided to replace the plugs while I was doing this.
Well, it turned out to be the driver side, farthest back. Problem solved , but I can't understand what caused it to go bad. I also found the sparkplug for that cylinder plus the one right in front of it had rust on the threads. Then i noticed rust on a few other pieces of metal back there.
I'd like to know what could be causing this rust and how to stop it.

 

I would just suspect that you are getting water run off from your hood. I would not worry about it and if you are put some sort of deflector under the hood to deflect the water.

 

I found my passenger spark plug at the firewall had rust on it just above the bevel seal. Hope it's like mentioned here, just water run off. I need to divert the water some how?

 

Check the threads having to do with a heater hose problem. Some models and engines have a heater hose back there that leaks and causes problems with plugs and coils in the pass. rear.