Sounds similar to my engine swap fun.
Did you remove the slave cylinder and compress the pin in with a c-clamp then bleed it while the bleeder valve was kept as the highest part on the slave? This made the difference for me. I bled mine twice THAN read the manual to find the proper method. :-) Oh by the way, I did pull my motor a second time before i figured this out. LOL
I suggest getting another pair of hands to help bleed. Do it the old fashion way too. Use the pedal, be sure whoever is pushing on the pedal gives it some pumps then holds the pedal down while you relieve the bleeder. This worked best. If the pedal stays down towards the floor, reach down and pull it up. Should only have to do it once or twice before it comes back up by itself.