There is no special Kaffarah to pay for delaying the khums payment. It is obligatory in the said case to pay the fifth of your net income that you did not pay khums from, by calculating the monies that you have and deducting what have you used in your needs and pay the fifth of the balance.
In this situation, the woman should have the ghusl of menstruation and she offer the prayers during the clean days. If she did not do so then she must offer the prayers as qadha. She should consider the periods of bleeding as menstruation, even if they were separated by clean periods.