Just to be safe, take a peek at the clutch adjustment procedure at Ack's FAQ (the link is in my signature).
Do a search for clutch.
Properly done, a Samurai clutch should work smoothly.
Usually, a bit of lithium grease applied conservatively to the moving/sliding parts of the shifter mechanism while installing will make things slide smoothly. Remember, the components that actually control the clutch do not rotate, so the grease (again, applied in small amounts) will stay put.
BTW, did you replace the pilot bearing that is pressed into the center of the flywheel?
Hope this helps!!