Were the hydrolic line and master completekly drained? If they were (or are new parts) it is kind of tough to "prime" the system. What works for me to get things started is to leave the hydrolic line off the slave and use a small screwdriver pushed into the end of the line to open the valve, and press the clutch gently a couple times to get fluid moving through the master and hose. If the slave was already full of fluid, it could have a bubble trapped in the system. The fluid in the slave won't let the air escape.
DONT press the clutch pedal unless the valve on the hose is held open, or the hose is attached to the slave.
If you have fluid in the system, check the simple things IS the resivior full? Is the push rod from the master still attached to the clutch pedal? Did the system work before you removed the trans? If not, or if you don't know, maybe it had a bad master before you started...