I know I would not be a fan of Ford if I spent $50,000+ on a truck, only to have to pony up several thousand more dollars to replace poorly engineered parts.
It would save them a serious beating on their reputation as well as more money down the road fixing them.
You mentioned them having the body off, they have to do that to get to the turbos and everything else because they packed it so tight. Removal of the heads to replace the head bolts, which are apparently a commonly failing component, requires removing the body.
As far as the problems with the engines, most of them come down to physics - they're trying to make more power with a smaller engine.
The loss of displacement means they have to run higher compression, more boost and higher RPMs, which in turn means higher pressures and temperatures.
Combine that with the absolute minimum amount of metal necessary to hold the engine together under normal conditions to save money (bean counters) and weight (fuel economy) and you end up with a bomb waiting to go off.
The emissions equipment just adds another, separate dimension to the complexity and potential problems.
What I've read is that they supposedly couldn't economically redesign the 7.3 to meet the new emissions requirements.
My guess is that they probably could have redesigned the top end of the 7.3 (which is what is most effect by the emissions requirements) for as much or less than what they've probably spent on the 6.0, 6.4 and now the 6.7 and all of their various problems.
But, we all know that newer is ALWAYS better...