An axel shaft is not the same as a CV axel. The trick to making sure the axel is in all the way is not really a trick as much as luck. Check out a video on YouTube regarding ball joint replacement via "1-A Auto". This guy is funny, but he'll tell you how he does it.
I had to replace my ball joints and this axel was a P.I.T.A.! But a little twisting and faith....it went in.
If the bearing does not mount flush, then it's not all the way in.
You can pop the cap off the box that the spline slides into to make sure that the bearing for the 4x4 is where it should be.
Sometimes if you don't jack the front end up high enough that bearing in the box will roll forward. Just raise it up more so the bearing stays out. After that try it again, and don't forget to talk dirty to it...Rams love that lol