Hamstrings work in conjunction with the quadriceps muscles. That burn you feel at the top of the thigh is the quad counteracting the hamstring.
Are you saying the pain is in the quads rather than the hammys?
If so, you're pushing too hard. Your quads have been pushed to the limit trying to make up whatever you lost in the hammys.
Back way off, only start when you're feeling 100%, and don't push it in the meantime. Otherwise you risk a quad tear. Believe me, you don't want this.