I'd consider Romer's logic here. Personally, I don't know if it's worth extracting the fuel pump until there's more evidence of the pump being the problem or just a symptom. The lack of a CEL or DTC P0230 (as per FSM) makes me think your problem is upstream, electronically. The FSM states that the fuel pump speed is determined by engine output which the ECM converts into a waveform for the fuel pump ECU (hence what you mentioned about 3 speed settings). Why does the ECM think the engine doesn't need fuel?
It's hard because I haven't really followed everything that you've done (my initial reaction was that it's time to take it to the dealer, but I can appreciate having a fun technical problem to solve when you have the skills).
Were you able to rule out sensors/shorts/electrical gremlins that would make the ECM believe there's something wrong with the input or output of the engine?
Lots of stuff here.
First, I agree with your line of reasoning.
If I replace the fuel pump, it would be after I figure out the root cause of the issue, and fix it.
My troubleshooting so far suggests that the pump stopping is a symptom, not the root cause.
Replacement of the pump would be primarily for preventative maintenance reasons. Sometimes the time and effort to get to a component makes me opt to replace it as a future time saver. Like when you replace a clutch that still has some life when you have the transmission dropped for another reason. I think of these as "while you are in there" jobs.
I believe I have ruled out electrical shorts, grounding, water intrusion, fuses, sensors and relays. Some of those are from visual inspection, others are from component bench testing, others are inferred from lack of codes in OBD/Techstream.
I think the ECM is happy with it's inputs. The risk is that I am missing something, because I don't know what to look for, or I am making bad assumptions.
The fuel pump is testing out good, at least from the tests I have tried from the fsm.
I'm leaning toward electronic control unit failure or erroneous ECU/ECM inputs. I don't like to guess though, so I'm trying to systematically troubleshoot and isolate until I get to a root cause.
Worst case, I put it back together and take it to the dealer. I'd rather not, since I feel like I should be able to figure it out with 'mud help.
I just have to wonder what the UN, an Australian mine operator, other severe service operator would do if stuck with a failure like this. It doesn't feel very Land Cruiser like. We should be able to fix these rigs with bailing twine and barbed wire!!