Hello Jummy,
My initial impression is that the problem may not be your hamstring itself but it may be a referred pain from either your lower back or gluteals. This would explain why the MRI is clear.
Have you a history of lower back pain? If so you may get more effect from stretching your gluts and lower back and performing some gluteal and core strengthening exercises. Sometimes mobilisations to the lower back and deep tissue massage of the gluteals can improve the pain you are describing.

regards
Rod
Fountain Gate Physiotherapy | Physio Narre Warren, Berwick, Hallam, Cranbourne and Beaconsfield.