I know the incision site has healed. But how long does it take for muscles to heal after a hysterectomy cause I still feel pain every so often.

Never the same again. Often a significant wound takes about 4-6 wks to heal, but it will never be the same. Once cut/injured, you will have a scar at the site and this remains and may bother you on/off for life. Some get adhesions and this can cause pain intermittently. Once healed, gentle stretching of the scar area to maintain its elasticity can help with contracture and thus reduce pain. Consult doc. Good luck.