Regarding your SELECT NEUTRAL fault... I would check the 'Low Range' switch in the gear shift assembly. It's buried down under the H gate, but you can test it with a multimeter at the transfer case ECU - Pin 33 of C1319. Testing it on continuity, with one multimeter pin on ground and one on pin 33, you should have no connection when the gear shift is in High range, and a connection to ground when the shifter is moved over to Low range.
I've seen it a couple of times where the switch has become gummed up and it sticks, so the transfer case ECU keeps thinking you want to switch range - which if it isn't in Neutral, you will get a SELECT NEUTRAL message up on the dash all the time. Failing that, have you tried swapping the transfer case ECU over from your parts vehicle? as the early ones are known for going pop, and it could be something internal to that.
Before the BECM/throttle pedal issue, did you have any issues with the gearbox indicators on the H gate or the instrument cluster not matching up what gear the shifter was in?
The throttle position sensor is a weird one - none of the connections on it go anywhere near the BECM - they go direct from the sensor to the connector under the bonnet and to the engine ECU.
I've just looked at the connector pinouts and the 2 grey connectors you show as having shorted pins on are all power outputs from the BECM - and again none of these are actually connected to the engine ECU that I can see. Most of them are outputs to the rear lights/door functions, power to the courtesy lights and RF receiver, FM aerial amplifier, Rear view mirror dip ignition feed, and RHF outstation/window/door amp power feeds.
The engine ECU diagnostic feed goes through one of the connectors in the RHF footwell behind the kick panel - it could well be worth checking that for a corroded connection. If you can get communication to the engine ECU, then you can swap the other ECU in and read the immobiliser code from that, and then program that into the BECM to allow it to start, and then check the throttle on that other ECU.
At this stage, I'd like to say you possibly got lucky and haven't killed anything on the BECM, but won't know until there are other tests done. I would ideally work on trying to get diagnostic communication to the engine ECU, as that will allow you to swap the ECU and then narrow down the throttle issue. Out of interest - can you talk to the ABS ECU on diagnostics? The BECM, HEVAC, Gearbox ECU, Engine ECU, and ABS Ecu's all use the same data lines - the all the ones you can talk to go through a splice in the dash wiring loom, but the ABS and Engine ECU go through the kick panel connector (which is known for corroding and having bad connections), so if you can't communicate with ABS either, then I'd start there. Once you can get comms to the engine ECU, swap it over, recode the BECM for the immobiliser code in the replacement ECU and see if the throttle works.
I haven't done much with the Diesel P38's, but once you get the comms to the engine ECU, you might even be able to read the live data in the current ECU, and see what it thinks the throttle position sensor is doing.