I'm willing to bet you need to adjust the pedal throw/pedal return adjustment. It can pull air into the line if you push past the piston's throw inside the master cylinder. I'm not sure of how much, but the pedal should be a specific distance off the floor/firewall, There should be about 3/4"-1" of spring tension to return the pedal before pressure builds as you press on it. Then the rest should be hydraulic pressure from pushing fluid to the slave cylinder. The way I bleed my brakes and clutch lines is,
fill empty bottle halfway with fluid,
put clear hose from bleeder screw into bottle AND submerge into the fluid. When you pump the pedal back and forth it pushes the fluid from the reservoir into the bottle and PULLS a little bit of the fluid on the back stroke.
So in turn you will have smooth, fluid transfer, as long as you keep putting fluid in the reservoir and the line in the fluid from the bleeder screw.
P.S. pedal throw is important for proper clutch engagement.
But It still sounds like when you installed the master and pedal assembly, the pedal stop adjustments are off.
Good luck
