This may sound silly, but did you check the bulb in the instrument cluster? (oops, it does come on). If the CE light lights when you start it, then the ECU should be considered functional. That is part of the self-test. If the ECU is dead, then the light will not work. Or at least that is how it should go.

I am still not convinced that these ECUs have a true backup mode. They may have some back up maps for when a sensor goes south, but the truck will not run if the ECU is toast or not powered. I think you are confusing a "limp" mode with a poorly running engine.

I also don't quite trust the quote in Chiltons. 1) It is Chiltons, 2) I would almost bet that paragraph is in every version of Chiltons. I am also very concerned with the "popping". ECU's should not do that and there are no parts in an ECU that should allow that to happen and for it to work at all.

What happens when you jumper the diagnostic link? Do you get any codes at all? 12?

With two ECU's and Occam's Razor, I would be more inclined that there is something else wrong, not two bad ECU's.

I know you have troubleshot this thing to death, but is may be time to start back with the basics. To some degree, what you describe sounds like a timing issue or it could be a fuel delivery problem. It also could be something like a clogged cat. It could be a TPS or IAS (or whatever it is that gets adjusted on the 2.8 family of engines). Engine temp sensor, especially with the change in cold idle. Just some ideas.

So, there are a few things that should be checked. It could be that whatever is wrong toasted the 2nd ECU, but that again is not quite as simple as something extra-ECU as being the source of the problem.

Good Luck,
Michael

PS. What did the old ECU "smell" like? Did it smell burned? It will be pretty obvious if something did fry.