Can stem cells from male convert to cells of female-only organs, and vice versa?
I am assuming you are talking about embryological stem cells and embryological development of genitalia. 

The answer is no. 

Male stem cells have XY chromosomes. Y chromosome is the sex determining chromosome with SRY gene that determines testes development. Absence of the Y chromosome leads to female development by default. That is why XX forms women and there are people with only one X chromosome which are women. (Turner's syndrome)

It might be possible that SRY gene undergoes a mutation and the gene isn't expressed. There are Y chromosome linked diseases. 

You should read up about Y chromosome and development of genitalia. 

https://en.wikipedia.org/wiki/Y_chromosome
https://en.wikipedia.org/wiki/Development_of_the_reproductive_system