you need to bleed the clutch master cylinder. Try the following:
Have a buddy get in and slowly depress the clutch in, same as if you were bleeding the slave cylinder. Once hes got it down crack the line fitting at the MC open almost all the way but still threaded open. Hold a rag under it as fluid will come out. Once it stops coming out, close the line fitting and have him slowry release it. this will bleed the air caught between the fitting and the MC port. If the pedal is still soft then the MC must be bled.
Get a bleeding kit from your local Kragen Auto Parts for $5.99 ( it will be labeled as a brake master cylinder bleeding kit, but it will work fine)
remove the line at the MC, and install plastic fitting and hose from above kit. Open the MC resevoir cap and route said hose from kit into the resevoir making sure it is submerged in fluid. Then, have your buddy slowly press the clutch pedal down and hold. Then very very slowly have him release it. Wait at least 15 seconds for the MC return springs to return and repeat untill no air bubles are observed from the bleeding tube in the resevoir.
Once there is no air reinstall the MC to SC line ( with clutch pedal in the "up" position). Then bleed the slave cylinder.
If the pedal is soft then it is posible something in the slave cylinder might have gotten damaged and it must be replaced.
Good luck mang, and make sure you never let the resevoir run out of fluid.
later