I am using the same Wilwood calipers, 1 1/8" bore Wilwood master cylinder and replaced all hard and flexible brake lines.
Once I have the pressure bleeder setup it takes less then half an hour to bleed the complete system and to get a rock hard pedal quite high up on its travel.
I didn't bother to bench bleed the master cylinder and figured if need be I could do it on the car.
Looks like the last thing it could be is your master cylinder.
Other thing is the system takes quite a bit of fluid. When I use the pressure bleeder I don't fill the actual bleeder tank I just keep the master cylinder topped up. This means I have to release the pressure from the tank, remove the top plate and top up the master cylinder at least six times for each of the front and rear circuits (making sure I don't run them dry).
Doing this I then know that the first master cylinder full of fluid is getting bled through the system and any air that may be high up in the system is getting forced out.