Let me back up
Let me back up and ask this...there are 2 plugs to the ecm...so is one plug 5v ref1 and the 2nd plug is 5v ref 2
I guess I'm thinking just to back up to beginning and go back thru it all
*wall of text warning*
I don't know the physical plug to pin numbers on this ecm. they are all labeled differently. Ref 1 and Ref 2 could be in 2 different physical harness to ecm plugs, or the same. it doesn't really matter, it would just be how the engineer that designed the board inside laid it out. the 2 chips that output 5v are probably side by side in there somewhere.
they use 2 different 5v circuits for redundancy for the fly by wire throttle and gas pedal. technically either one of the 2 chips could burn out, lose the 5v and you'd still have throttle control. the old cable throttle only has one position sensor, they needed to add a 2nd since it's possible these could stick open with a lost of signal from a bad sensor.
so we would need a schematic of the ecm itself, which is almost impossible to find and would be pages long, so all I can do it guess from what the troubleshooting software says.
so my take is the ecm has 2 transistors, probably some kinda FET really, but either way. 2 electrical components that output a very steady state sold 5 volts. this is used to power the sensors. the return from the sensors is less than 5v varied by whatever it's designed for. like say for instance your 2.3 volts in the return wire. the ecm will turn that analog 2.3 volts into a digital number. usually 0-255. I don't remember why 255, something to do with 2 digits of hex. (above my pay grade) but left over from when ecm's didn't have a lot of space and computing power so space was kept at a minimum. anyways, off topic. sorry.
that 2.3v needs to be very specific, so much so that the ecm also supplies a sensor ground on a 3rd wire. it could easily just ground to the engine block or something saving time and money. but it can't because you get small voltage drops from a ground like that. it needs a known ground and 5v. so that it knows that 2.3v signal is correct.
so from reading this about your fault codes..
1. Ignition OFF, disconnect the harness connector of all the sensors connected to the 5-volt reference bus
*(bus is what they are calling the circuit. ref 1 is one 5v bus, ref 2 is another 5v bus)* for the applicable DTC. Refer to Circuit/System Description.
2. Ignition ON, test for 4.8-5.2 volts between one of the 5-volt reference circuits and ground.(in the plug, not the engine block, even thou that might be useful info too)
IMPORTANT: A short to voltage on the signal circuit of certain components may cause this DTC to set.
1. If less than the specified range, test all of the 5-volt reference circuits for a short to ground. If all circuits test normal, replace the ECM.
2. If greater than the specified range, test for a short to voltage on all of the 5-volt reference circuits, or the signal circuit for each component associated with the appropriate 5-volt reference bus for a short to voltage. If all circuits test normal, replace the ECM.
3. Connect each component associated with the appropriate 5-volt reference bus, one at a time, while monitoring the voltage. The voltage should not change more than 1 volt.
1. If the voltage display changes more than the specified range when a component is connected, replace the component.
and you saying you're seeing above 5.2v on the 5v ref 1 and Rev 2 circuit. that rules out most of what the trouble shooting expects. it expects the more common low voltage by a sensor shorting internally to ground and dragging the voltage low. but you have high, which is harder cause where is that voltage coming from? either a short to voltage inside the harness or ecm. but it's very odd to me that it's only a few tenths of a volt and both 1 and 2 read the same.
so at this point. I'm not sure what else to check that's easily done. I would hate to say change the ecm like the guide jumps to without exhausting all ideas to test. they are expensive, requiring programed to the truck by a dealer level scanner.
I would make sure you're checking the 5.5v at the sensor plug with a good multi meter, not just going by what the scanner says?