Alright final update for this “problem”, as this thing just continues to confuse me. I finished getting this rig ready for sale with the last round of upgrades and set it aside for photos. As I was intending on parting ways with this thing with the diagnostic lights still on, I photoed the thing running hooked up to a display to show the machine functions, except this was what surprised me: the diagnostic lights are gone. They flash briefly on startup and shutdown but they no longer stay on like they used to. I have absolutely no idea what caused this as the only thing I did was install a GPU and Mojave, let the thing sit without power for a day, then plugged it back in and viola! I’ve power cycled this thing several times since just to see if it decides to jack with me some more but so far it seems happy. Hopefully this escapade helps anybody who runs into a similar fluke, though I’m still unsure what started it in the first place. Cheers.