Given your situation, we strongly recommend reviewing the laws of staining. It is important to remember that not all stains will render a woman niddah nor invalidate the clean days. See our article on stains for more details.
While tehorah, you should wear colored underwear (or disposable pantyliners) and wait at least a few seconds (ideally 15 seconds) after urinating before wiping. After intercourse you should wait a few minutes before getting up and/or wiping yourselves, and do not look for any staining. Be sure to use colored sheets and towels to avoid finding problematic stains.
During the clean days, you should change your white underwear more frequently to prevent any staining from accumulating to the size of a gris. You may reduce the number of bedikot to the hefsek taharah, and one bedikah each on days 1, 7, and one of the intermediate clean days (a day that you are less likely to experience staining). You should bring any questionable stains to your rabbi for evaluation. Do not assume a stained bedikah will invalidate the clean days; there are many shades of brown that are acceptable.
You can ask your doctor if there are ways of reducing this irregular staining. Please ask if trying bioflavonoids (1000mg, 3x/day while staining) or ibuprofen may help reduce extended staining.
Please feel free to get back to us with any further questions.
B’hatzlacha!
This response has been updated to reflect the rulings of our current Rabbinic Supervisor, Rav Kenneth Auman, regarding waiting before wiping.