Good point. If the new flywheel is thicker than the old one, the pressure plate will be further back in the bell housing.
Another possibility is that the distance from the surface of the flywheel to where the throwout bearing rides is greater than it should be. It is sometimes interesting the little differences that crop up with replacement parts...
It could be that the pressure plate is enough further back that its trying to push the throwout bearing further back than the clutch fork and the push rod from the slave cylinder will let it go.
When you loosen the mounting bolts for the slave cylinder, is it being pushed out by the rod?
If so, remove the bolts and try fitting it back in by hand. When you first feel some resistance, measure the gap between the mounting surfaces. refit the slave cylinder with enough washers on the bolts to hold the gap you measured.
Try the clutch then. Adjust the number of washers as needed to get the clutch operating properly, then measure the final gap you come up with between the mounting surfaces.
Remove the cylinder and cut that much off the end of the rod that inserts into the cylinder. Round the end off like the origonal end and reinstall everything without the washers. DO NOT LEAVE IT WITH JUST THE WASHERS.
That "should" solve your problem assuming all this is the problem.
If nothing else, the push rods are cheep and easy to find, and its a heck of a lot less effort to try it than to pull the engine and transmission out again.