Can you read the OBD2 code for cylinder balance and see if there is any discernible pattern.
I know it says random, which would seem to contradict any specific pattern, but it might make diagnosis easier if you could get any more tidbits of information.
Test compression and leak down to confirm mechanical integrity.
Swap the injectors from the original engine?
Possible false diagnosis code due to differences between year of manufacture of the engines. Check connections of the replacement engine to see that they match the original.
regards
Mech
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