When you remove the cap is there any pressure release? Make sure the holes are clear in the master cyl. Not sure what you have, if it's a remote reservoir, but if you had some gunge blocking a passage in the master, iut will do just that-build pressure and not allow it to release.
Are you using old lines, or did you replace the OEM ones? If I had a problem like you describe, I would break things down into their component parts, and ensure that each line is clear, tests clear, and can sustain continued air or fluid passage at a volume or pressure commensurate with what you would expect. Same for the master cyl, same for the slave cyl. I might go as-far as to remove the entire system with the possible exception of the metal clutch line attached to the chassis, and hook the whole thing up, and test it for correct function. Blowing the rigid line out and being able to see that the airflow is consistent, doesn't lessen or plug-up should confirm the rigid line is OK.
With the system hooked together off the bike, you should be able to see that everything works. Or, that you find the problem.
I've had internally-collapsing rubber brake lines on trucks and cars, and bikes too, you would expect that if you do your own work on used vehicles over 50 years of driving and riding probably a similar number of vehicles.
Did the clutch lever ever get hard to pull like a brake lever? That's a sure sign of a plugged relief hole.