I don't understand why this seems to be a reoccurring issue, but the same thing happened to me. In my case, it was my first dual disc clutch from SouthBend. After install, it was a bit... booger - getting it into 2nd or reverse. I've since replaced it and the new one is much easier, but I also had the transmission rebuilt (new syncros and bearings) at the same time, so I'm not sure which one made the difference.
One thing you might check. Remove the slave cylinder from the bell housing and reach in and grab the release fork end and check for fore/aft play. You should have at least, say, 1/4" play front to back (in the direction of the cylinder's plunger motion). If it's tight, you will have a problem down the road. No play indicates there's already preload on the clutch fingers. This will cause the clutch to "wear out" early.
The solution, unfortunately, is to grind the back of the release bearing. This is not something you want to hear now, since the transmission is already in place, but it's straight from Peter's mouth. I'm not sure if this plays into the problem if shifting into gear, but I have to wonder. I ground a substantial amount of material off the back of the bearing on mine and shifting into gear is much easier - though reverse is still a challenge occasionally. But as I said, I had the transmission rebuilt, too.
Some said the shift issue due to pilot bearing drag. Yet, when I removed my first clutch where I had the shift problem, the bearing was free and rotated smoothly. So, I don't really know.
More conversations with Peter, maybe.
-Jay