Assalamu alaykum Ustadh Ahsana Allahu ilayk So a few days ago I thought my menses began so I didn't pray for 5 days. Then on the fifth day my real period came and I realized it might just have been Istihada. Do I have to make up all prayers?

What you are certain you left while you were pure, you make up, and what is only doubt and guessing you leave and do not turn to it, and this is what Imam Ibn Baz rahimahullah said. The sign is that the blood of hayd is thick and dark and has an odour while the blood of istihada is thin and yellow, so the days are judged by that and by your usual habit.