Based on your description, you may continue counting your clean days from your Wednesday hefsek. Since your final hefsek was acceptable, and the toilet paper may be disregarded, you may continue with your count. In general, we do not recommend making numerous attempts at a hefsek, since it could irritate you (which is possibly the source of the staining you later found on toilet paper). However a clear hefsek is valid even if found after repeated attempts.
For the future, you may find it helpful to clean yourself out well prior to performing the hefsek to clean out any old blood. If you have time, you can take a warm bath. Even if you are rushing, you can clean internally with a wet bedikah cloth. It is best to do this at least 20 minutes before attempting a hefsek to give your natural secretions time to return and reduce the risk of irritation.
Please feel free to get back to us with any further questions.
B'Hatzlacha!