Air was likely in the line because it was not at the bottom.
Once the master and the line are bench bled it should seriously take about 5 bleeds on the slave (usually 3 does it) and you are done, there is not much air in a slave cylinder to begin with
I have my helper pump the clutch pedal SLOWLY 5 times, on the 5th press I open the bleeder SLIGHTLY and let the last 3-4" of his foot/pedal travel force all the air and then fluid out.
The next time I wait for helper to press clutch 5 times, hold pedal, then open bleeder. Repeat this 4 more times = done
This is the proper way to bench bleed the master cyl and hydraulic line:
It can take FOREVER
Seriously we have spent 45 minutes to an hour doing this method, its a pita but it does work., You can watch those little air bubbles come out for a long time and its really hard to depress the master cyl plunger by hand
Now I just set it all up just like in the video, above except I just open the master cyl and pull the plunger until brake fluid comes out all the way to the top (Split second)
Then press the plunger back in, put master back together and done
For me this has worked every time, new parts right out of the box shipped dry.
If you have air trapped in the line you need to get the master above the line, reservoir above that. Now wrap on the line with screwdriver to release the bubbles.You can watch the air make its way up and out of the fluid in the reservoir, some bubbles are the size of a needle point and some are size of a green pea.
You do not need to open the quick release/spring loaded fitting on the end of the hydraulic line. If you do, it should be in a jar of fluid so no air can go back up inside.
The hydraulic line will be fully purged of air when you hook it to the slave and bleed the slave. Getting all of the air out of the master cylinder before it is installed is the key here, once installed that air bubble is trapped.
A leaky slave cylinder is usually the problem child with these systems, or a bad seal in the master. People get in deep when they try to re use an old slave or TO bearing, or keep the same master and add a new slave, or again when they use crappy defective parts right out of the box.
Never use a cheap slave! I know I said this before but I have dropped a trans, installed a customer supplied slave and weeks later we are doing it again.
This happened a couple of times and now I will no longer even mess with cheap auto parts store crap here.
Use Ford or Luk (OEM).
Also if I am going to drop a trans I am going to install a new clutch (pilot, driven disc, pressure plate, TO bearing), new slave and new master pretty much every time....