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The hamstring tightness is likely to be unrelated to epididymitis. This may come from pinched nerves from back. Physical therapy and passive stretching are likely to help you.
The epididymitis symptoms may take 2-3 weeks to resolve completely. So some residual symptoms at two weeks are not unusual.
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Since there is an aggravation; the best would be to get the culture of semen and urine. These would be able to point out the best antibiotic efficacious against the residual infection. These culture need to be performed after 48 hours or more of antibiotic free period. That way the best culture reports would be obtained.
The urinary passage and semen (sexual) passage are common when they terminate. So cross infections are not uncommon and it is a more or less an academic exercise to label an infection primarily as urinary or sex organs related. For all practical purposes they are treated in same fashion / duration.