Welcome to my world.
I did the same change out this past summer and I have the same problem. When cold, the clutch operation is smooth as silk, but as soon as the system reaches operating temperature, the clutch doesn't seem to want to engage/disengage smoothly. It takes a full throw of the pedal to release the clutch - meaning clutch pedal against firewall! When cold, this is not necessary.
I am not sure what the cause is and I have no answers for you, but if you do find the problem please list it or contact me.
I installed new MC and Slave, replaced the nylon hose with braided SS, checked the movement (cold) approximately 9/16" (center hole, checked for hole wear at the pedal and the radius arm - all checked out fine. Now that winter is coming on, I will again pull the tranny to re-inspect everything that I did inside. I have driven the car this way since June and it appears to be getting a bit better which leads me to believe that there must be a binding situation between the front cover and the TO carrier (all new also) The original TO bearing carrier was bronze (and somewhat worn - ergo the change)but the new one (Moss) is steel with some type of protective coating. I removed the coating on the inside and polished the cover prior to assembly, but did not measure the clearance between. I will do that when I pull the tranny again. I coated the interface with a bit of white lithium high temperature grease hoping this would not degrade and find its way to the clutch plate.
Another possiblity that was mentioned to me was that the clutch plate may be spreading apart when reaching temperature, but there would be no way to verify that unless I develop some sort of xray vision.
Also, during the original install I opted to use a cross shaft from a TR4A with the grease fitting and the shorter bushings - two on each side, which seemed to to provide a "truer" fit. A new fork/shaft pin was installed and the TO pins in the fork were also replaced. Like I said earlier, everything was replaced for new with matching(or so I was told) parts.
I sure hope you find the source because I have scratched my head until I have no hair left.