It is not only permitted, but halachically encouraged to clean yourself as thoroughly as possible before performing a hefsek taharah. The purpose of the hefsek taharah and moch dachuk is to establish that uterine bleeding has stopped. Cleaning beforehand is encouraged so that old blood in the vagina should not mislead us into thinking that bleeding continues. Some women use a douche for this purpose. However, please consult with your doctor before doing this. It should only be done if you do not find that it causes any irritation. It's a good idea (not an absolute requirement) to wait at least twenty minutes after washing before the bedikah in order to allow the natural moisture to return, and so that you are more confident that bleeding has ended.
It is halachically acceptable to leave a moch dachuk in for extra time, but we do not recommend it. Even if you are not certain about cessation of bleeding, the whites worn overnight and the morning bedikah pretty reliably reveal any additional bleeding. Please be cautious about leaving in a tampon for long periods in the future (being careful to follow package instructions). This might pose a risk of Toxic Shock Syndrome.
The size of a stain on a bedikah or tampon does not affect its status (this is different from the rules of stains on garments). It sounds as though there is a good chance that the color would be acceptable. You are correct that this requires evaluation by a rabbi. If you are comfortable sending the moch to a neighboring rabbi in whose rulings you have confidence, then we suggest you do that.
To allay your concerns about the color, recognize that the halachic status of niddah is not equivalent to menstruation. The Torah itself stipulates that some colors of blood render a woman niddah and some do not. If yours falls within the "not niddah" category, then its timing and place of origin make no difference.