You deserve a lot of credit for your efforts to follow these laws scrupulously!
Not all colors put a woman in niddah, invalidate a hefsek taharah, or pose problems during the clean days. This is the case with some browns and may well be the case with the stains you describe.
Unfortunately, you cannot evaluate the stains on your own. You need an expert opinion. In this day and age, there are many ways to do this. Many rabbis accommodate women who wish to have their stains evaluated anonymously. Ask the synagogue office for information. Alternatively, you could send your husband to drop off stains for you. We do not think you should rule out the rebbetzin. Although she did not discuss bedikot with you, she will probably be very pleased to see that you have begun to perform them. A female orthodox friend could also help you to ask your question. If you would like to contact a Yoetzet Halacha, click here for a directory outside of community Yoatzot outside Israel, or please write for referrals in Israel.
Bedikot are best evaluated in person. However, when this is difficult or impossible, we recommend Tahor App, which uses special color calibration technology to ensure that a photo of the bedikah is accurately transmitted to a halachic authority. It is available on iPhones and some Android models.
However you ask the question, be sure to indicate what the stain is (a stain on underwear, hefsek taharah, or bedikah), the stage in your cycle, and any other factors. In this case, it is important to mention how long you have been niddah, how many failed hefsek taharah attempts you have made, and your PCOS status.
We hope this helps and that you do not hesitate to contact us again. We also wish you success with your medical treatments.
This response was updated August 2020.