Multiple codes/limp mode

What voltage readings are you getting at the DME? Thats the only way to rule out a wiring issue. You have to load test circuits as well. You can't just look at them and say they're good. That DME relay is the main power source for all those sensors/actuators codes. You need to focus on that DME and do real testing or you're just going to end up in the same place every time. Have you even checked the voltage level at any of those fuses coming from the dme relay? I don't understand why you're just throwing parts at this without testing.
Use a 12-volt light bulb to load test power circuits, see if they can carry current. You need to if these 3 pins are getting power (load tested) and if those grounds are good. From the battery all the way to the dme.

Okay. Well, you should have left the DME plugged in and back probed the connector, sorry I wasn't clear on that. The B+ on Pin 13 with it unplugged is just the control side of the DME relays power, if that connector was plugged in with the key on that would read 0volts because it would be pulled to ground. But you're saying on connector X6003 Pin 1 you only have 2.5volts? The 2nd diagram is going to Pin 1 on X6003. That should be 12-volts all the time. Key on or off. There's an issue.
Where are you seeing X6002 fuse 1 is wake up signal?
But X6003 Pin 1 (red/Black wire) should be 12-volts all the time coming from Fuse F4 10amp.
You should test with the connector plugged in and back probe with a T-pin. Check that F4 Fuse though, even with the ECM unplugged that should still be 12-volts.

Awesome, finally found it. Thats not even a diagnostic mistake, who would have guessed that someone else took a fuse out. I couldn't find any#50 fuse either. And there is no terminal 50 anywhere I see. But that F87 was a main power feed to the DME, That was causing those sensors to lose power and therefore setting all those codes. But do keep an eye on that Fuse. Someone took it out for a reason, if it kept blowing on someone there may be a short to ground somewhere that's intermittent. A wire rubbing on ground due to running vibrations or something like that. Watch to see if the terminals on the fuse get dark, that will mean it's getting hot, just not enough to pop the fuse yet.
Thank goodness. I was losing sleep over this one bud.

The DME probably lost its memory after a period of time with that circuit powered up and eventually it was seeing bad signals from the cam sensors and such, then it just lost its mind. Glad you found it. At least you know if that circuit pops that particular fuse that the circuit is the one going from F4 to DME Pin 2. I am wondering about the 2.5volts, but that's for another day. It's been fun.