This thread is fascinating/terrifying. So... At this point, maybe calling Mercury tech support is in order?
Oh Ya, I'm pretty sure that's probably the only option. But the people there at tech support who have access to the needed information won't talk to the consumer. They will only talk to someone who has a CDS G3 and the only people allowed to have G3 is a dealership tech. silver_power won't be able to answer the questions tech support will ask.
The PCM part numbers that are posted look to be a "blank" PCM. These are PCMs that don't have any software installed. So when silver_power asks if they are the correct PCM, the only answer anyone give is --- maybe/maybe not. But tech support will know based off of the G3 report what software is installed. Tech support will also be able to help the dealer tech determine if all the CCMs and TVMs are correct and have the right software installed.
I know you said the power steering fluid is full, but the 1st generation of Axius has a very specific way to fill and bleed this system, if that wasn't followed. That could very well explain the pressure faults you see.
You said you repaired the wiring harness? I don't know what you did for the repair. But these data harnesses are considered not repairable and are replaced when they have a problem.
You asked about the power supply to the computers. All the computers in this package get at least 2 and sometimes 3 wires supplying power to them. They get 12 volts from the "keep alive" power and also get 12 volts to wake up.
You asked about the correct procedure to reflash and check software versions. Yes G3 can do this if the right hardware is in place. It is fairly complicated, if I remember right we spent the better part of the day covering this in the Axius class. The handbook we got at class spent about 40 pages covering this. Way too much information to cover in a forum.
I understand you losing confidence in mechanics. Some are better then others. But I'm guessing you will need to find the right one to get this problem fixed. Generation one Axius isn't a bad product. Once it's working properly. ALL of these computer controlled engine packages are very touchy when it comes to 12 volt power, ground and the wires that connect them.