It may sound obviuos but have you double checked the clutch pedal end of things ??
With the cable engaged in the pedal but not to the gearbox, it may be worth checking that the pedal & inner cable are free to move enough to give you the desired amount of travel
Also worth checking the cable routing .... If you have a very sharp kink in it, it'll be very difficult to depress the pedal .... The cable will be wanting to fold in half, rather than pulling the inner cable through the outer sleve
As said very difficut to diagnose the problem without seeing things in person.