I had (sort of) implied in Game, Set, Match that Lois's memory/amnesia issues had been compounded by drugs. The new body didn't have those drugs in its system, therefore Lois's memory issues were 'cured'. Something else to be mentioned in the next section.
And I think Lois would adapt to a male body a little better than Clark would to being female - Lois has gone undercover as men and although this would be an extreme case of going undercover for her, she does have some familiarity with the differences in body language and attitude.
Clark, on the other hand, has probably never even considered actually going undercover as a woman.
