I'm sorry, what part of my reply led you to imply I was dishonest and unethical?
Even if they know what the "real story" is, as you claim (and they might) doesn't that just take us straight to the beginning of my reply- you want to pay (guessing) $5k for them to put in a whole new wiring harness in your car to make SURE they get all potential trouble areas?
What makes you assume paying $35k for a car guarantees it will "run right"? I'll be the first to admit they built a lemon here and in a perfect world there would be a series of campaigns done on these to mitigate these issues. It's not unheard of for manufacturers to build such lemons and allow dealers to quietly make a killing repairing them, with the only customers not paying full pop the ones who pursue the complaint process fully. When it goes on long enough it usually hurts them, probably will here too.
I'm just not following your logic here. If I buy a car for $25k does that mean it can run bad?
As for the new PCM I wouild imagine the technician was directed to replace it by the flow chart diagnostic in the factory manual. I can't comment on whether yours was actually bad or not.
I would advise anyone with one of these trouble prone vehicles to purchase a factory service manual, as published by Daimler-Benz. The 2001 edition for instance is 1600 pages, Amazon showed 7 used from $75, the new one is probably a bit over $100 but as that's just a little more than an hour labor charge at the dealer it will pay for itself quickly.
The Chilton and Haynes manuals are better than nothing but not by much, especially for complex electrical problems. The factory manual will have the benefit of not just schematics, but diagnostic flow charts, functional block diagrams of systems, parts location images or mapping, and the pinouts and locations of various connecters in the harnesses.
Subscriptions to online services like AlldataDIY are okay but I find their menus can be dodgey to navigate and having to stop working on the car and go to the PC (and print out pages or even figure which you might need) is too easily a diversion when you can have the whole book at your fingertips in the driveway or garage.