Did you replace the hoses all around? I hope they are not original...
Are you using a power bleeder or the old fashioned way? I would highly recommend power bleeding. The one time I encountered the symptoms you describe it was due to some air trapped in the rear brake circuit. A good full bleed with a power bleeder cured the issues.
Bleeding with the pedal can also quickly send an old master cylinder to the grave yard....ask me how I know. 
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