The people you are dealing with sound like complete morons, either that or cunning businessmen. I vote for a little of both. The way you spot someone who doesn't know what they're talking about is when they try to assign humanlike qualities to something they don't understand. Wiring harnesses don't "go bad"--they are not replaceable items. they do not "get possesed". It is never "hey it would be a good time now on that car to replace the wiring harness". They aren't even considered an item. It may be an item to the dealership in that it has a part number and can be ordered and installed in exactly 11.25 man hours which equates to X dollars of service revenue, but they aren't an item in the troubleshooting sense. What are they going to do next, replace the computer? "Hey Noah must be a bad computer, we should probably replace it." Or, "a bad frame, and engine, have to replace that too."
Rubo thought you were talking the entire wiring harness, maybe you are, if not, the engine harness can be replaced while the engine is in the vehicle.
If you had a problem with your engine would you throw away the entire engine? No, you might want to consider finding the problem first right?
My advice would be to find another dealership. Are you even under warranty?? You're not right? Why are you even going to a dealership? Here's lesson number one about dealerships. They sell cars so they sell service with the same mindset. They do not earn their reputation in the community based on the repair business, it is based on the selling cars business. They earn customers by selling cars then they try to tack on as much extra work as possible to sell more labor hours for repairs. I have two friends that work in sales in the service department. they make commissions on selling stuff you don't need. Everybody has to make money, and I can't fault them for that, but you really should consider having repair work done at a place where their work is the basis of their business.
I would have the dealership replace the intake manifold gaskets then find another shop to examine the other symptoms if they even continue. My guess is they won't.
The construct of an OBD II computer is such that it has no way to explain to a human being what is happening during an unexpected event. Air entering the system that is not accounted for by the MAF, TPS, and IAT sensor is going to throw off the combustion and timing events such that you'll get misfires. I bet it is the intake manifold gasket and your wiring harness is not posessed by the devil.
