Mazal tov on the birth of your baby!
We are sorry to hear of your prolonged niddah status.
The duration of staining when adapting to a new pill is unpredictable. However, that should not keep you from getting to the mikveh within a reasonable period of time.
Staining does not necessarily invalidate the clean days. We recommend making an attempt at a hefsek taharah. The hefsek taharah need not be completely clear, so browns should be brought to a halachic authority for evaluation. In this situation, the moch dachuk may be omitted and you may perform only one bedikah per day. Any questionable bedikah cloths should be brought to a halachic authority for evaluation. If there are further difficulties, please get back to us or a halachic authority about further reducing the bedikot required.
Stains on undergarments should also be evaluated. If the stain is light brown with no hint of red, or if the stain is smaller in area than a gris (roughly, the area of an American dime or Israeli shekel), then it does not invalidate the clean days. Changing undergarments more frequently than usual may help keep stains larger than a gris from accumulating.
If you are taking the progesterone-only pill, you may find it helpful to take the pill at exactly the same time each day. You could also contact your doctor about temporary measures to reduce staining, such as taking an extra half-pill every twelve hours after the regular one.
Our telephone hotline is another helpful resource.
We hope this helps. If these measures are insufficient, please contact us or a rav to discuss other possible measures.