The minimum wait is connected to when a couple were last permitted to have relations. Therefore, day one of the five days is typically the day on which a woman became niddah (and relations were prohibited) or the day on which she begins to conduct herself as niddah out of doubt about her status.
Since relations are prohibited on an onat veset, if there was no time that a couple were permitted to each other between a prior veset and the beginning of niddah, the woman may begin counting the five days from the veset.
If you became niddah before halachic sunset on Sunday, then Sunday was certainly the first day of the five days, with a hefsek taharah scheduled for Thursday. But if you became niddah only at night on Sunday, then there was some time at the beginning of Sunday night when you and your husband were permitted in relations. In that case, a hefsek taharah would be scheduled for Friday.
Your case is a little tricky. When a woman discovers blood at night, we usually assume that the bleeding began at night, even if it might have started during the daytime. Therefore, it sounds as though you had some time when relations were permitted after sunset on Sunday, before you discovered were in niddah. This would make Friday the earliest day for a hefsek taharah. If we have misunderstood the situation, please get back to us with more details.
Assuming that you were supposed to make the hefsek taharah on Friday, the one you did on Thursday still counts. However, you should begin counting the clean days from Friday night, with immersion scheduled for this coming Friday night. Please get back to us if there are any other considerations involved (e.g., shalom bayit or fertility concerns).