So I have the exact same scenario on my car. PO installed a valeo SMF/clutch, when the transmission sh*t the bed and I had to replace it, a sachs clutch kit was installed.
Now clutch pedal will not go all the way to the floor.
The guru who did the work told me that the reason was the valeo flywheel is slightly thicker than the one that would have been installed with the Sachs kit. The throw of the slave cylinder is essentially shortened because the throw out bearing was shifted closer to it. The car shifts fine, and has a very light clutch pedal. At the time I had been without my car for a month and was completely fed up with the whole process so I said I'd just take it and fix it later on my own if it became an issue. So far I've put 50k on the car that way with no issues (knocks on wood).
Sorry, the hydraulic system does not get new operational specs with a new clutch installation and change to match a different operational range. The bearing position changes slightly from old and worn position to new clutch position. All components being correct, installed spring tip height moves away from trans a little bit with a standard (not self adjusting clutch) clutch.
Master cyl stroke move X amount of fluid, X amount of fluid moves slave cylinder X distance. The only real designed in variable is the starting point of the fork based on bearing position from the new clutch. Its a little bit like a brake master cylinder, it moves the caliper piston the same with new pads or worn pads.
Do you have any noises associated with pedal as it approaces the floorboard with engine running that GOES AWAY if you bring the pedal slightly up?