Clutch replaced and gears still not work efficiently

I have a 2002 Civic Ex with roughly 92k miles. I have been having issues with the clutch. I had the Slave Cylinder replaced, and still had the same issue. As the car will not go in to gear I then was told that I had about 5-10k miles left on my clutch. So I had the clutch replaced with a aftermarket stage 2 competition clutch. Now I still have problems sometimes with it going in to 3rd and 4th gear. About 60%-70% of the time it will go in without any problems. However other times it does not want to go into gear. After pumping the clutch onve it will go in to gear or if I put it in to gear slowly. I also feel as if sometimes it does not go in all the way. Once I then put it in third gear there is a slight vibration of the shifter when I keep my hand on it. Most times if I take it out of gear and put it back in to third gear it will not do it. What else can I do? The place where I had the clutch replaced said that it might be a transmission problem, someone else had mentioned that it could be in the linkage. I took the car to the Honda dealership for a Diagnosis and they did not find anything wrong.