Sorry that I don't have any real constructive input to offer.
I can tell you that I have read a whole lot of posts on this & another Dakota site regarding to buggy computers & problems related to suspected buggy computers; however, most of the posts I pay the closest attention to are on the Gen2s.
I've read a few theories about the PCM failures; someone once said that they were related to where the PCMs are positioned in the engine compartment & heat being an issue but I'm not sure I see that, someone else said that they mostly had questionable solder joints going on. . . .
My own '03 Dak suffered a PCM failure back in (I think it was) '18 with 60 some K on her, & at the time I thought that was rather premature. Of all of the potential causes that you listed from that article, my Dakota had/has none of them.
After my troubleshooting pointed at the PCM I did some research to help me decide what to do, & I remember watching a Youtube in which the Youtuber was saying that he had had so much bad experience with reman Dakota PCMs he didn't trust them at all & he felt that the remans were mostly coming from Dakotas that had been scrapped & the people selling them were simply doing the most cursory & rudimentary checks on them & then selling & shipping them as remans . . . I don't personally know if there is any truth to any of that.
I did elect to send my PCM out for diagnosis & repair. The facility I sent it to told me they found a broken solder joint on a pin & they told me they also replaced a coimponent in the coil driver circuit, & I seem to remember it being a transistor, but I cannot be absolute positive about that. They charged me about $100 and change (I could check the actual receipt) & did claim a lifetime warranty on the work that they performed & I haven't yet needed to see if that will hold up.
It also seems possible, after reading your OP, that your current problems might be happening somewhere else on your bus system. My '03 is on the PCI Bus, but that ended in (I think) '04, & I think your '06 would be on the CAN Bus system.