I don't know if you are looking for just niddah alone, but if you are open to exploring multiple aspects of Rabbonus, you might want to consider Rabbi Leib Keleman's CKD (Center for Kehilla Development). Based in Yerushalayim, the center is set up as a five-year post kollel programme and includes specifically shimush in various areas.
It's blurb here writes:
The Center for Kehillah Development provides a post-kollel, five-year immersion in Shas and Poskim. Avreichim are tested repeatedly on over 900 daf gemara, receive shimush and guidance in darchei psak, pass the written and Oral Semicha examinations in Issur V’Heter, Hilchos Shabbos, and Hilchos Niddah, and they take private smicha examinations from the most prestigious poskim and batei din in Eretz Yisroel. The curriculum includes limud b’iyun in Nefesh HaChayim, Daas Tevunos, Kisvei Rav Yisroel Salanter v’Talmidav, Maamrei Rav Yerucham Levovitz of Mir and Kisvei Rav Shlomo Wolbe. Throughout their five years at the Center for Kehillah Development, avreichim participate in a classical mussar vaad, give regular chaburos in Chumash and Mussar, and teach at other yeshivos in Yerushalayim. All avreichim participate in year-long courses in Chinuch and Sholom Bayis, and several times each year the CKD conducts seminars in CBT and other psychological interventions and support systems.
As far as the shimush aspect it is worth noting that those on the programme have access to HaRav Osher Weiss shlita and receive practical shimush in hilchos niddah from the renowned posek, Rav Ephraim Kirschenbaum, shlita. (See here)