My 20+ yrs experience ( 1977 ~ 1999 ) as a Ford Parts mgr was mostly involved with DSO built heavy trucks.
My experience was that the DSO build process had not changed much from the mid 1960's,
they still used a similar DSO form as as used for SAI.
As noted the rear axle, the calipers, brake proportioning valve, etc were DSO parts.
IMHO the engine was a RPO ( regular production option ) assembly, pulled off to a re-work station where the intake & carb were installed.
This "rework" would not effect the regular engine production line, but still used the quality & material controls of the plant.
Since SAI would untimely be the Manufacturer of record, documenting the content of the car was on SAI, FoMoCo was in this case a "sub-supplier".
Still the central question of how the re-worked engines were then identified from Cleveland, into San Jose, and into "special build" cars destined for SAI is unknown.
Unless documentation surfaces confirming the Cleveland engine "code" 554J was altered/changed, I believe they were "DSO" marked like a color X or a special tag
that differentiated the assembly from RPO engines.
just sharing my observations that may add understanding,.... or not
regards,
jim p