The clutch hub may not be sliding freely on the transmission splines. If it doesn't slide freely on the splines, it will be held against the pressure plate or flywheel enough that it won't disengage. This can happen if there is a burr or damage on the transmission input shaft or on the clutch hub. The clutch can also hang up on the spline if the transmission weight dangled on the clutch during installation. That would distort the hub so its no longer true to the clutch disk.
You say the flywheel was worn. Is the replacement flat and true?
If you start the car in gear with the clutch pushed in, does the clutch otherwise operate smoothly?
