I'd more then bet when you installed the clutch/gear, that it isn't seated all the way to the case bearing. If this is so the clutch assembly will protrude out too far and rub the cover. As you tighten the nut on the clutch and have it tight, take a hammer and tap on the clutch. Now is the nut can tighten more then it wasn't seated to the bearing. You may need to do this a few times.
Here you will see that I use a 1 1/2" socket to seat the clutch should I have to. Notice the socket is forcing the inner portion of the gear, and a even pressure is applied to the hub.
The 3 pins are hidden by the socket.