I actually just posted about this a week or so ago. I was having a similar if not same problem as you are. My clutch master cylinder was leaking fluid and so I replaced that and my clutch and flywheel. I am now shifting as smooth as brand new. If I were you I would check your master cylinder and see if you are leaking any fluids. If so that could be the reason why your not being able to shift very well. Because the master cylinder isn't being able to disengage your clutch all the way enough to make a smooth shift. Well it worked for me. I also found a strange piece of metal in my clutch as well and, that could have also been the problem. But I would definetly check your MC.