Is it permissible to refer to the genitalia by their names during intercourse with one's wife? And does this constitute "rafath" (obscene or indecent speech during Hajj)?

There is no legal impediment to naming the private parts between spouses during intercourse. This falls under the permissible "rafath" (intimate talk) between spouses. "Rafath" refers to any speech related to women, and it may also refer to intercourse, as in His Almighty's saying: "It has been made permissible for you the night of the fast to approach your women."