Did you take the clutch apart only to file the dents smooth?
Was it working before you took it apart? By working I mean disengaging and not clunking too bad into first. Just filing those dents flat shouldn't change anything except make it engage/disengage a litlle smoother. I don't understand why you changed from a 1mm to a 2mm pusher shim.
There would be. You'd feel a lot of "stiction" with the clutch on the bench. "Feelings" don't mean much.I've had the clutch pack in my workbench and used that to 'open' the clutch. The plates still didn't want to slide over each other. There is a great deal of ''sticktion'' between the friction and steel plates.
I think you are putting it back together wrong. Everything has to go back on in the right order and facing the right way or it will do what you are describing. I ususally have to try 3 times before I get it right