1988 Chevy Corvette Clutch Master Cylinder

I have a 1988 corvette with a doug nash 4+3 transmission. I recently had the transmission replaced with a rebuilt 4+3 from a 1984 corvette. During the swap, a new throw out bearing was installed and the clutch looked fine according to the mechanic. Since the swap, I occasionally have to pump the clutch to build enough pressure to change gears, and when stopped, have to pump it to get into first gear and in reverse. Sometimes while driving (with higher rpm's) the clutch seems to work fine, while other times I may have to pump it a couple times to change gears. I have replaced the slave cylinder with the same results. The system has been bled numerous times by myself as well as by the mechanic. He now suggests maybe replacing the clutch fork? Could it be possible that the master cylinder is bad? The clutch worked just fine before the swap. Thanks.