I'm wondering if it could be cleat position? It seems like your pain has happened since they were installed. Just something else to consider, in addition to many other possibilities!
Personally, I would not stretch an injured hamstring. I'd just let it heal, and take ibuprofen. I probably would do a really easy ride, but I'd stop if it hurt at all.



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Tomorrow will shoot for 40-50 miles and see how that feels. My fitter raised my saddle a couple of MM yesterday, which was part of the problem.