Aside from the alarm, I had exactly the same issue. Thankfully, after much head scratching Matt Bentley got it sorted for me. I went through all the diagnostics you've done but it turned out to be the actual connectors themselves. The female side of the connectors are not sprung loaded so if they have opened too much or corroded, the male side will not make a good connection and this brings up the fault.
2 options:
1 - Take a look at the connectors at the throttle, loom of doom and throttle body and try to close up the female connectors or replace them
2 - Drop it off at MBR and let him sort it. He'll be an expert at this now