Don't know about the rest, but I can answer this:
Also, why does Holly have the female face?
Short answer: he performed a sex head change on himself.
The reason for this is explained by an extremely fast scrawl in the first episode of season III.
The scrawl, in full, reads (my emphasis):
RED DWARF III
THE SAGA CONTINUUMS
THE STORY SO FAR...
Three million years in the future, Dave Lister, the last human being alive discovers he is pregnant after a liaison with his female self in a parallel universe. His pregnancy concludes with the successful delivery of twin boys, Jim and Bexley. However, because the twins were conceived in another universe, with different physical laws, they suffer from highly accelerated growth rates, and are both eighteen years old within three days of being born. In order to save their lives, Lister returns them to the universe of their origin, where they are reunited with their father (a woman), and are able to lead comparatively normal lives. Well, as normal as you can be if you've been born in a parallel universe and your father's a woman and your mother's a man and you're eighteen years three days after your birth.
Shortly afterwards, Kryten, the service mechanoid who had left the ship after being rescued from his own crashed vessel, the Nova 5, is found in pieces after his space bike crash lands onto an asteroid. Lister rebuilds the 'noid, but is unable to recapture his former personality.
Meanwhile, Holly, the increasingly erratic Red Dwarf computer, performs a head sex change operation on himself. He bases his new face on Hilly, a female computer with whom he'd once fallen madly in love.
And now the saga continuums
AND NOW THE SAGA CONTINUUMS...
RED DWARF III
THE SAME GENERATION
To find out more about the events explained in the scrawl, you need to see the final episode of season II.