The eeprom data is encrypted just as I though so even if you read the data out and had the correct software to change it it wouldn't work as the data is encrypted.
Correct.
I would need to find out the decrypt key. Could hook it up to a logic analyser to get the key out but then I wonder how many bytes the key is?
The keys are different for every company they supply the encryption boards to. But even knowing the keys wouldn't help without also knowing the decryption algorithm which of course will be unique and non-standard.
And they don't just decrypt data lines, they're encoding some address lines too, so the encrypted byte at address $1234 in the ROM won't necessarily end up at address $1234 when read by the ECU.
Do you have any info on any of this e.g data sheets etc?
You can get datasheets for the PIC and GAL easily enough (though they sand the ID off the top of the GAL and encase the PIC in resin/glue on later boards) but anything beyond that would have to be worked out.