Picked up a 2004 5 speed a week ago and it has a strange issue with third gear. It shifts into gear perfectly fine with no noise at all but sometimes once I shift into third and let the clutch out it will grind. To avoid this is I push it into third really far it will engage correctly. I am thinking maybe something shift cable related. Any ideas? New clutch and fluid is good by the way..

Did they change the slave cylinder with the new clutch?

Slave cylinders are notorious for going in these cars. Or maybe they did not bleed out the system all the way if they did replace it.