You could buy the correct P&E Multilink for the CPU together with their "PROG Flash Programming Software". You might be able to read the Flash from a good unit and then try to program one of the bad ones. If it can read the good ones, but can't even talk to the bad ones, then you know the CPU has been damaged.
Here's a "universal test". Are chips on the bad boards getting hotter than the good ones? Or running colder?
How does that KTAG connect to the ECU? Does it connect using the debug port, or does it connect to a communications port on the main connector and in the vehicle loom? I gather it provides options to do both. Which one were you using?
If it connects via the loom, then it needs working firmware to read the Flash. If it only connects to that (and not the debug port), then it must be able to program the Flash via that comms port. If it only connects via the debug port, then it may have damaged the chips somehow if it can't then talk to the CPU to read the Flash. The only way I could see that happening is if it supplied out-of-spec voltages (over 5V) to the debug port.
Some Motorola/NXP/Freescale (name changes and company purchases) chips that have Flash inside the CPU need 8V or 9V applied to one of the debug port pins in order to program the part. Some of the MC6808 variants do this. It is possible the programmer did this when trying to program (applied a high voltage) which could have damaged the CPUs.
If you can buy those CPUs, then it should be possible to get them replaced on those boards.
> All of the incorrect voltages (2.7 and 2.54 volts) that were being seen at different
> sensors and relay points, were all originating from the 2 ECUs
With a meter or an oscilloscope? If they are programmed as outputs and are generating 2.5V and not oscillating, then that indicates the CPU has been damaged. If they're oscillating (you can only see on an oscilloscope, although the AC or Frequency range of a meter might show this) then the CPU may be rapidly running and resetting resulting in those outputs doing that.
> pushing 2.7 volts to some of the onboard transistors instead of ground
That's a valid way to drive transistors. You can have resistors on the board generating 2.7V and have the CPU drive the output to ground when it wants the transistors of. That's unlikely as the transistors would be on during power-on and reset, so there's a problem. Or the 5V output could go through a resistor to turn the transistor on, and after that resistor you might get 2.7V. But don't make too many assumptions.
You should have enough information (or hints as to how to get it) to know if the new hardware damaged the ECUs. If that's the case it shouldn't be your problem now.
For those interested, here's what it looks like. An MC68376 in its natural environment:
https://ecu.design/ecu-pinout/pinout-campi-29f400bb-lamborghini/
Tom