ok, i cant read the blog but from what i am reading i will mention a few things. you can tell me if you think its relevant. or helps in any way.
The MGB may have been changed, but do you know it was PH III or just guessing? either way, it is only the upper casing of the gearbox that is new. the rest could have been an O/H box. when fitting a new MGB, the inputs are removed and fitted to the replacement. therefore could be thousands of hours in use with no O/H.
if an engine and an input get chip warnings at the same time weather both new both old or a mix of the two. they are coincidence. neither is connected to the other in anyway except for the high speed drive shaft and the fwd support tube.
build debris is often found in new or O/H gear boxes, but we know that and take it into account. but it is not unusual to get a chip light on our a/c though rare on or 92's, but if it does happen then a servicabilty check is called up.
if the chip light would not go out, i presume they checked it and if they found nothing on it then its a fault somewhere else in the system more likely.