How does this gross change happen?
Hormones and epigenetic changes.
What is this transcript change and how does it manifest itself?
The transcript is what part of your sex chromosome and other chromosomes are read and transcribed to proteins.
it happens by hormones binding to cell receptors and the repression of other signalling pathways.
What of the phenotype to they now share with the opposite sex and how did this occur?
They share skull size hip size hand size hight blood, secondary sex characteristics etc that are expressed within their family among females males etc.
What do you mean they are sufficiently the other sex?
I mean the physical traits they express are sufficient to categorise them as phenotypically female for the reasons I've stated above.
What do you mean the majority of the physiology criteria?
I mean a criteria that can be used; that takes into account all other aspects rather than the ability of primary sexual function the same criteria we use for others whose phenotype and genotype don't match.