One thing to check - and it's preetty easy - is the snap ring that goes on the end of the axle. It is located right under the locking hub cap.
If you forgot to ire-install the snapring, the axle can slide in or out causing the birfield joint to not be centered on the axis of the kingpin rotation. This, along with worn kinpin bearings can cause intermittant noises in the steering.
Then again, it's possible that you didn't set the wheel bearing preload right and they have worked themselves loose.
I can't count all the stupid things that I have done to my Samurai... That's how one learns somtimes.