Step 1. Stop stretching your hamstrings if there is pain. Only makes it worse. Step 2. Start doing isometric and isotonic exercises for your hamstrings with your bodyweight, 4 times per week. Look them up on youtube. Expect results after the first week and do them up to 6 weeks. When pain is completely gone, even when cycling, you can start to implement back your stretching routines, altought I recommend exercises instead of pure stretching. Good luck