The Hydra won't fix the software compatibility issues. They need to be flashed within certain versions as it's a protocol issue as stated earlier. Older versions use a different protocol and won't speak to a newer flash.
As long as the ECM and VPM you ordered are within a range of versions it may talk to each other, but since they are likely all coming from different buses, sizes, etc, the ECM will just use default values and the bus will run, but will be speed limited. even if the VPM is dead. VPM needs to be plugged in but if only the VPM is dead the ECM will work in default mode.
This was the state of my bus when I bought it. ECM worked, IDM worked, VPM did not. Was completely dead. They had to get 4 other VPM's till one would work with my ECM, then they were able to update all 3. ECM, IDM, and VPM software wise so they are all on a 2024 year version calibration/protocols/etc.
Again you may get lucky, and all 3 be within each other version wise and it may just work. If the VPM works though, it's gonna run your bus differently because it's vehicle personality values (VPM = Vehicle Personality Module) May think it's a truck or a smaller or larger bus, and try to run your bus in a not so great way.
If you get ServiceMaxx Godmode, you can set the EFRC code which if they came from another bus may already contain the NavKal calibrations you need, and you just need to set them and you just need to set the EFRC Code value and HP values and you could be good to go. So you could get lucky with your ebay purchases of the ECM/VPM. But if the Calibrations on the VPM are wildly off base it could cause problems with engine running.
The ECM is easy to get correct, buy it for a T444E. Plug it in, and it should work even if on an old version. With a dead VPM it will run default mode safely. You'll just have a "WARN" light because it cannot read the VPM, but it should crank. Once done, Assuming you put in a working VPM, this is where trouble could ensue if the VPM came from a wildly different bus type. Most of the 3box's were dt466E's or T444E's, if the VPM came from a T444E, functioning wise it should work alright without issue, you'll just have some slight issues like Cruise Control may be disabled, or speed limiters may be enabled, VIN number won't match the body, and the important the EFRC code likely will be off limiting Horse power changes.
ServiceMaxx Godmode can fix all of that assuming the scenario I just outlined where the VPM and ECM match the bus type and engine, it likely will have the proper calibrations already installed, you just need godmode to set them.(Set the EFRC and HP). Send me a private message with your number and I can walk you through what I know on it.