I am having this same problem right now. I have an 85 C20 with NV4500. The master is stock 87 and the trans is a 99 with internal slave. The square body master doesn't seem to have enough volume to completely release the clutch. I can see it pushing the throw-out bearing and I can even get a feeler gauge between it but it's not pushing it down far enough to completely disengage.
I have been looking at some Wilwood masters with a bigger bore, but they all only seem to have a 1" stroke and I don't want to have to move the pivot point on the pedal if I don't have to. Today after work I am going to try and get some volume numbers. Has anyone figured out the best way to mount a newer master yet? I can fab something up, but would rather find something that will bolt up.