Oh man I have learned a lot on this. So I have an extra ECU. I bought it at the local yard and it is the EXACT part number for my rig per Vin#. I swapped it and another from the yard, twice both...so I am pretty familiar with the process now as you can imagine.
Both of these yard ECU's would crank but not fire. Utterly confused and without any help from the yard guy (who also thought this was before the era of flashing etc.) I started calling around, the dealer, mechanics etc. So in 1999 the LIMITED model only had the ECU "flashed" or correlated to the keys somehow. To get the other yard ECU to work I would have to get it "flashed" or "coded" to my current keys. And then, only that one would work...you can't have more than one flashed to the keys for some reason. So, since the yard guy will not take this back I have this ECU but would have to pay another $150-200 to get it flashed. Ugh.
So I put this on hold for now but I have the ECU. The one in my truck says it's "Remanufactured for Toyota by Denso." I don't like that, it's not original. the dealer convinced me though that it's because at some point someone lost keys and had to get a reman to go in there. He and another mech are saying it's so doubtful it's the ECU at all...sort of it works or doesn't and this one in the truck...the reman it does work. So we'll see. My mech said he'll chase the circuit back before trying the other ECU.
Anyway, that's the story on that.
I think replacing the harness is your best bet considering your situation. BUT, you'll have to see when you get in there. If it's crispy then that's a good sign that's likely it. Mine was not which was actually concerning since my codes (both banks) were intermittent too. I guess the only risk is time...having to crack back into it if that doesn't do it. Since I paid my mech to do that I'm out the money. And the funny thing was I did it to save time (I actually wrench quite a bit but am working and coaching full time.) LOL, if I'd only known because now without coaching I could have tackled it myself.
LMK how yours goes.