Imagine how I feel. Due to a major house fire, I drove 21 miles round trip to sit in my library's parking lot, (29 degrees F.), To use their wireless internet so I could offer my knowledge and experience for your benefit, as well as a dozen other people who need my help. You provided a few clues for a starting point, but sooner or later you're going to have to figure out what is making the clicking noises or you're going to have to do some tests and give me the results to analyze, then I can determine where to go next. What exactly am I supposed to do with "a clicking noise under the dash"? What you need is a live mechanic, who you pay by the hour, to observe for himself what is happening. He will do the things I can't do over a computer.
You said this problem comes and goes. That can apply to intermittently low system electrical voltage due to a discharged battery. Low voltage confuses computers and makes them do weird things. The battery can cause this as well as a problem with the charging system. In my first reply I asked you to measure the battery's voltage. I don't know why you won't do that so I can rule that out. It has nothing to do with whether the battery is new or not. It could have to do with why it isn't being recharged while you're driving. An intermittent generator problem can result in that new battery running totally dead after just one hour of driving.
It would be irresponsible for me to guess as to a cause and send you on a wild goose chase, but apparently you think that's how we solve strange electrical problems. The last thing we want to do is unintentionally insert additional variables or make the problem seem to go away without knowing what we did to do that. When it acts up again, we won't know what "fixed" it last time, so we'll have to start all over with the diagnosis, at $100.00 per hour.
I appreciate that you were considerate enough to make a donation, but understand I spend just as much time with anyone I think I can help. A few of my conversations have involved well over 50 replies over many weeks before we figured out the cure for the problem. In those cases the car owner had to make tests and take measurements, then tell me the results. Sometimes I spend hours digging through grossly-over-complicated wiring diagrams.
What you need to do is ask for a refund if you don't think I can fix your truck over a computer. If you can't figure out how to do that, I'll contact the site owners on your behalf. I don't know how to ask for a refund since I've never done it, but I have never heard of anyone having a problem. They want you to be happy so you'll come back again.
You didn't say anything about slow cranking speed when trying to start the engine, so based on that, I'm leaning toward the charging system is okay. It also appears there are no noticeable symptoms while the engine is running. I'm bypassing a lot of diagnostic steps and will share what I've run into before. You'll have to decide if it's worth pursuing. Ford has had problems with their pickup trucks with water leaking around the windshield and dripping onto the "GEM", (generic electronic module) under the dash. That is their version of a Body Computer which they feel is necessary to do the things we never needed a computer for before. Check if that computer looks like it has been wet and look at the connector to see if there's any corrosion between multiple terminals. Even a light film of corrosion can be enough to conduct current from one terminal to another and make a circuit try to turn on. At the very least, you can unplug that computer to see if the symptoms stop.
Thursday, December 3rd, 2015 AT 5:39 PM