Get a flashlight, lay on your back on the DS floor, shine the light on the bracket that holds the clutch pedal, look for cracks in the bracket. Also check the firewall around the where the CMC bolts to for cracks in the firewall.
If there are cracks, the movement does not allow the pedal to depress the MC all the way which in turn does not allow the MC to send enough fluid to the slave cylinder to compelty disengage the clutch causing drag and hard shifting.
It can be fixed, but it is not an easy fix.