Mazal tov on the recent birth of your baby!
As long as you wait at least a few seconds (ideally, about 15 seconds) after urinating before wiping, you may disregard any stain you find on toilet paper and are not rendered niddah. You should also take care to wear colored underwear and use colored sheets, so if you do experience any staining on the underwear or sheets it may be disregarded.
Additionally, you should wait a few minutes after intercourse before getting up or cleaning yourself and try not look for any staining.
To help prevent the pain, you should certainly use the lubricants suggested. If that does not help, following your physician’s recommendation to use Estrace makes sense. The Estrace you are referring to is simply a topical estrogen cream. Even if some is absorbed into the system, small doses of estrogen are not a problem with breastfeeding, especially for an 8 month old. He is old enough to be eating foods as well as nursing, and thus if there is a reduction in supply (the only concern about estrogen during breastfeeding) the gap can be filled with food. Please note that Category X refers to dangers in pregnancy, not breastfeeding. The concerns at each time period are not the same.
Please feel free to get back to us with any further questions.
This response has been updated to reflect the rulings of our current Rabbinic Supervisor, Rav Kenneth Auman, regarding waiting before wiping.