Not clear what your plot device here is... but here are some suggestions.
If John is John in the beginning, then we realize (Through dialogue) that he is in the process of becomming "Kate" - then when he FIRST assumes the role of KATE, I'd double slug the names
JOHN/KATE
Thereafter slugging 'her' name as KATE for the rest of the script.
This is the same for 'revealed' identities - The MASKED MAN at the beginning of the movie is revealed to be SAM PARKS when he removes the mask
MASKED MAN/SAM PARKS
Thereafter - the character is slugged by his 'identitiy' in the scene IE SUPERMAN or CLARK KENT